Abstract:Triticeae crops mainly include common wheat, barley, rye, oat and Triticale etc. These species usually host a complex genome with huge size (>5.1Gb, with >80% repetitive elements), thus resulting in establishment of high-quality genome reference behind other cereal crops such as rice and maize. Taking advantage of achievement on sequencing methodologies along with dramatic decrease on the sequence cost, studies of the Triticeae genomics have become reasonable, and breakthroughs in population genetics, pangenomics, and epigenomics have been made. These achievements enabled better understanding of the genomic variation and selection, and also provided resources to decipher the origin, domestication and local adaptation as well as assist genetic improvement of modern varieties. This mini-review summarizes current status and research trends in the Triticeae genomics in the past few years, and proposes the hotspots in post-genomics era in Triticeae crops.

Abstract:The narrow genetic basis is the major bottleneck for wheat genetic improvement. To broaden wheat genetic resources by using beneficial genes from related species is an important way to produce new wheat germplasm resource. Chromosome engineering is an effective approach to introgress wheat foreign targeted genes into wheat genomes. Homoeologous recombination and ionizing radiation are two high-effective techniques for inducing wheat alien chromosome translocations, both of which can induce chromosome structural variations in a short period of time and have been widely used in practice. This study briefly reviewed the progress of Chinese Spring ph1b mutant and 60Co-γ-ray irradiation on mutagenesis characteristics and application in wheat germplasm innovation. Combination of oligonucleotide FISH will facilitate introgression and accurate identification of alien genes, as well as improve the efficiency of chromosome engineering. This study provides useful information for further mining and application of wheat alien genes via chromosome engineering for broadening genetic basis and promoting studies in genetics and genomics of wheat.

Abstract:Horticultural crops are widely subjected to abiotic stress conditions such as extreme temperatures, waterlogging and high salinity. The harsh conditions seriously destabilize their growth and development and limit their adaptability and geographic distribution. Genome-wide association study (GWAS) is an effective approach by associating the genetic variations with the phenotypic variations. Over the past decade many genetic loci/genes have been identified by using the power of this approach. GWAS results can serve as a foundation for deciphering the genetic architecture and identifying candidate genes for functional study, and breeding new varieties via gene pyramiding. In this review we represent the principle, characteristics and influencing factors of GWAS, its application in studying of abiotic stresses in horticultural crops, as well as the prospective for exploring the functional genes in future.

Abstract:Fagopyrum cymosum（Trev.）Meisn. is a perennial medicinal plant (designated as buckwheat) of the genus Fagopyrum of the family Polygonaceae. In order to analyze the geographic distribution characteristics of wild F. cymosum in China and their genetic characteristics, relying on the Third National Survey and Collection of Crop Germplasm Resources, we conducted a survey in 13 provinces and 62 counties (cities and districts) in China. A total of 530 F. cymosum germplasm accessions were collected. The wild F. cymosum resources were found to be widely distributed in China, especially in the areas of E 90°.44′28″-119°.36′37″, N 24°.59′66″-33°.53′16″, with a preference in the subtropical monsoon climate area below 3500m. The inter-population diversity was observed regarding to the population quantity and genetic characteristics of F. cymosum, forming the distribution characteristics of high-altitude special type concentrated distribution area in Southeast Tibet, low-altitude genetic diversity enrichment area in Southwest China and low-altitude genetic type single area in the middle and lower reaches of the Yangtze River. There are many excellent materials in the wild population, which can be developed and utilized in the fields of medicine, health care, animal husbandry, sightseeing and breeding. This study provided important reference in rare plant protection, taxonomic evolution of buckwheat, innovative utilization of germplasm resources and crop genetic improvement.

Abstract:In this study, 14 phenotypic traits including single grain weight, cross-diameter length and longitudinal diameter length of 55 chestnut cultivars were measured. However, no significant differences on morphological traits in subsets of chestnut varieties were observed, and it is difficult to identify the varieties accurately using phenotypic traits. We designed SSR markers based on chestnut genome, followed by PCR amplification of 55 chestnut species and data analysis using the software POPGENE32, PowerMarker V3.25 and NTSYS V2.10. By taking use of six pairs of SSR primers with good polymorphisms, 31 alleles were detected and the percentage of polymorphic loci was 100%. The mean values of polymorphism information content index, Nei’s gene diversity index, Shannon’s polymorphism information index, observed heterozygosity and expected heterozygosity were 0.651, 0.696, 1.358, 0.524 and 0.703, respectively. According to the SSR-based genotyping results, 55 chestnut cultivars were classified enabling the construction of their fingerprints. Collectively, this study deployed the phenotypic datasets and SSR markers to decipher the genetic diversity of chestnut varieties and generate the molecular ID cards, which provided theoretical references for the variety identification, rational utilization and effective protection of chestnut germplasm resources.

Abstract:Foot rot of sweetpotato caused by Diaporthe destruens is a new disease in the southeast coast of Zhejiang Province. In order to explore resistant germplasm resources and explore the method of resistance identification in natural induced field, We investigated and identified the resistance of 126 sweetpotato germplasm resources, and analyzed the changes of disease symptom in late growth period of sweetpotato and effects of resistance on yield loss rate of fresh storage root.. The results showed that the control variety Zheshu255 was high resistant, Zheshu 38 was resistant and Zheshu 13 was high susceptible.Of which, no high resistance germplasm were identified among 89 new collected resources and local main varieties only 3 accessions were resistant, when over 65% of the resources were high susceptible. 13 resistant accessions were identified from the 34 progenies of resistant variety Zheshu255, including 6 high resistant and 2 resistant accessions. There were significant changes of disease symptom in the late growth period of sweet potato, especially the disease index sharply increased from the growth period of 120 d to 135 d in moderate resistant and susceptible germplasm. The disease grade of 93.8% of the total susceptible plants was 4 at the growth period of 135 d. Eventually, most of the susceptible plants rotted throughly at the base of stem or died . The yield loss rate of sweetpotato with good resistance (high resistance or resistance) could be controlled below 15% , while the yield loss rate of susceptible varieties was over 65% , even no harvest. In a word, the resistant germplasm resources of foot rot disease of sweetpotato were scarce, the good resistant breeding materials could be obtained through the conventional hybrid breeding of the resistant parents, and the incidence and disease index might be used as the identification index of resistance to foot rot of sweetpotato in natural induced field.

Abstract:Black spot (Alternaria sesami) and capsule rot (Alternaria alternata) of sesame, as one of the most important diseases, seriously cause the reduction of yield and quality in sesame. The identification and evaluation of sesame germplasm resistant against both diseases were carried out by artificial inoculation in the field, in order to provide elite parent resources for disease resistance breeding and guidance for disease control. In 2020 and 2021, the 84 sesame germplasm resources were evaluated for resistance to both diseases. 15 accessions were resistant to black spot (R; 17.86% of tested resources), and 29 accessions were moderate resistant (MR; 34.52%). 30 accessions were susceptible (S; 35.71%), and 10 accessions were highly susceptible (HS; 11.90%). No accession showing immune and highly resistance (HR) was identified. For capsule rot, there were seven accessions showing highly resistance (HR; 8.33%), 25 showing resistant (R; 29.76%), 26 showing moderately resistant (MR; 30.95%), 22 showing susceptible (S; 26.19%), as well as four resources showing high susceptibility (HS; 4.76%). Six accessions, such as Hunan sesame, 97-6, Liaozhi 9, Liaopinzhi 2,Ganzhi 11, Jizhi 1, were resistant to both diseases. The number of resistant resources to capsular rot was significantly more than the number of accessions showing black spot resistance.

Abstract:Increasing planting density has become an effective way to improve soybean yield. However, the comprehensive evaluation system to identify density-tolerant soybean germplasm resources has not been systematized. This study attempts to construct an evaluation method based on multi-year data, followed by evaluating the density-tolerant characteristics to identify the elite soybean germplasm. Seventy-seven soybean germplasm resources suitable for Huang-Huai-Hai ecological area were sown with two densities including high-density sowing (plant spacing 8.0 cm, about 315,000 plants/ha) and conventional density sowing (plant spacing 13.0 cm, about 195,000 plants/ha). The evaluation of dense planting tolerance was conducted by obtaining nine relevant character indexes in two calendar years (2019 and 2020). Compared with the conventional planting density, the height of gravity center and bottom pod of the plant were significantly increased (P < 0.01) and (P < 0.05), respectively, and the number of effective branches and seed weight per plant decreased significantly (P < 0.01) under high planting density. According to the significant correlation coefficient, the principal component and membership function standardization analysis were carried out to estimate the comprehensive evaluation value (M) which was deployed for the clustering analysis. The dense planting tolerance characteristics were divided into five types (I, less dense type; II, strong less dense type; III, intermediate type; IV, strong dense type; V, dense type). Three soybean varieties (Wuxing 1, Motte*, and Gaozuoxuan 1) qualified for condensed planting were preliminarily identified. Collectively, this study established a density-tolerant evaluation method useful for developing new dense-planting varieties and studying their physiological mechanism in soybean.

Abstract:The soybean variety Heike 56 was selected from the offspring of the hybrids of Heihe 33 (female parent) and Heihe 34 (male parent) in Heihe Branch of Heilongjiang Academy of Agricultural Sciences through sexual hybridization and genealogy. In the adaptive cultivation zone, this variety would take 105 to 110 days from seedling emergence to maturity, with the effective accumulated temperature (≥10℃) of 2030 to 2100℃. This variety shows the following phenotypic characters: sublimited pod habit, plant height 69.6 to 75.0 cm, branched, white flowers, pointed leaves, gray fuzz, pod sickle shape, brown when mature; round seeds, yellow seed coat, light yellow seed hilum, shiny, 100-seed weight 16.5 to 19.0g; protein content 38.80 to 43.05%, and fat content 18.18 to 19.69% (mean value of 5 years datasets); resistance against gray spot disease (grade 2, R), and moderate resistance against viral disease (grade 3, MR). It is qualified to be cultivated in the lower limit of the fifth temperate zone and the upper limit of the sixth temperate zone in Heilongjiang Province. Through pedigree analysis, its cytoplasmic components was derived from ‘Keshan Baimei’, through 9 transmission processes in 12 rounds of breeding from the 3rd to the 12th (Keshan Baimei→ Zihua 4 → Harvest 1 → Heihe 54 → Heihe 4 → Heijiao 7710 → Heihe 9 → Heihe 18 → Heihe 33 → Heike 56). Its nuclear genetic components might be traced back to 14 ancestral parents (two excellent foreign germplasms, five backbone local varieties from northeast China, four locally breeding lines, and one wild soybean germplasm), with the contribution rates: ‘Bei 92-28’ (25.00%), ‘Shi Sheng Changye’ (15.36%), ‘Heijiao 83-1345’ (7.81%), ‘Yubilei’ (7.81%), ‘Heihe 51 (L)’ (6.25%), ‘Suoyiling’ (4.69%), ‘Keshan Baimei’ (4.30%), ‘Keshan Silijia’ (3.91%), ‘Silihuang’ (3.71%), ‘Jinyuan’ (3.71%), ‘Heihe Glycine Soja 3-A’ (3.13%), ‘Hejiao 75-861’ (3.13%), ‘Heilongjiang 41’ (3.13%), ‘Changye 1’ (3.13%). Collectively, the abundant genetic diversity of ‘Heike 56’ has laid the genetic foundation for the high and stable yield, high quality, strong stress resistance and super-wide adaptability.

Abstract:To obtain new potato germplasm with high yield and high starch content, the tetraploid cultivar ‘jizhangshu 12(G12)’ was crossed respectively with three cultivated diploids showing high starch content. Three cross combinations were performed and each cross combination was divided into grafting group and control group. Grafting was conducted at the seedling stage between the tetraploid cultivated species (scion) and diploid species (rootstock), and pollination by the male parent (rootstock species) at the beginning of flowering. In the grafting group, an average of 254 flowers were pollinated to produce 112 fruits, with an average fruit setting rate of 44.1%. In the control group, an average of 296 flowers were pollinated to produce from 65 fruits, with an average fruit setting rate of 22.0%. Of 177 fruits, 30 seeds were cultivated to regenerate 15 F1 plants. Nine, four and two plants were verified to be tetraploids, triploids and diploids respectively, by deployment of flow cytometry analysis, chloroplast count and pollen mother cell chromosome counting methods. Genotyping using simple sequence repeat (SSR) markers showed that all tetraploids and triploids were hybrids from both parents. All the interspecific hybrids grew well, whereas only one line succeeded to produce seeds by selfing. The potato tuber size of interspecific progenies was significantly larger than that of diploid parents, and showed light to medium on the bud eye depth, with great improvement to that of diploid parents. The color of potato flesh was mostly yellow, and some interspecific hybrids tuber skin color differed with that of their parents. In the field trials, the starch content of all tetraploid F1 lines were significantly higher than that of ‘G12’, where no significant difference in yield was observed except one line ‘SY18-6’. According to the characteristics of tuber yield, starch content and starch yield, six lines ‘SY24-1' (starch content: 21.39%), ‘SY18-1’ (21.37%), ‘SY24-5’ (18.35%), ‘SY18-4’ (20.28%), ‘SY24-3’ (18.29%) and ‘SY69-3’ (18.84%) showing high yield and high starch content were identified.

Abstract:The content of oleic acid and anthocyanin is an important target for quality breeding in peanut (Arachis hypogaea L.). In this study, a high-oleic acid peanut line with pink testa "G110" (G, ♀) was crossed with a landrace line with purple testa "Purple Pearl" (Z, ♂). Kernels of both parent lines on 30 days after flowering (30 DAF, G1/Z1) and 45 DAF (G2/Z2) were sampled for the transcriptomic analysis. The differentially expressed genes (DEGs) enrichments in oxidation-reduction process (GO:0055114) and fatty acid biosynthetic process (GO:0006633) were observed. The gene ahFAD2B (arahy.5913QL) was up-regulated in G110, while another gene ahFAD2A (arahy. 42CZAS) was not significant difference (p > 0.05). AlleleXa/b and AlleleYa/b genotyping results showed that “G110” was aabb and "Purple Pearl" was AABB. By taking use of kompetitive allele-specific PCR (KASP) markers A004807 and 4004808, 66 high-oleic acid plants of genotype aabb in F2 populations were obtained, followed by self-pollination to F7. Of them three superior accessions namely 18-B-40, 18-B-49 and 18-B-54, with purple testa and high-oleic acid were identified, in which the oleic acid content was 79.52%, 78.84%, and 78.02%, 1.77 folds (p=3.61×10-9), 0.99 folds (p=1.21×10-9) and 0.99 folds (p=1.45×10-9) higher than that of "Purple Pearl", respectively. The oleic to linoleic ratio (O/L) was 14.69, 11.91, and 10.90, which increased by 11.58 folds (p=4.01×10-15), 9.37 folds (p=7.92×10-15) and 8.58 folds (p=4.51×10-15) compared with that of "Purple Pearl". The anthocyanin content was 30.87 OD/g, 29.16 OD/g, and 14.51OD/g, which increased by 23.91 folds (p=1.17×10-7), 22.77 folds (p=4.00×10-10) and 23.06 folds (p=1.63×10-10) compared with that of "G110". Collectively, this study obtained peanut germplasm accessions showing simultaneous enrichments of anthocyanin and high oleic, which might have implications for enriching high oleic peanut germplasms in China and future uncovering the mechanism of peanut oleic acid metabolism.

Abstract:In this study, eight agronomic characters (including plant height, leaf number, panicle length, panicle diameter, panicle weight, grain weight per panicle, branch number per panicle and grain number per branch) of 160 foxtail millet germplasm resources were investigated at three environmental conditions (Ledong, Hainan province; Luoyang, Henan province; Gongzhuling, Jilin Province) from 2015 to 2016. Their broad-sense heritability were estimated by simultaneously considering the years, latitude environments and genotypic variations, and the genetic relationship among these traits was analyzed. The average heritability at each of eight traits using single-factor analysis method was over 0.9 at years and latitude environments. While no variation on individual heritability at eight traits was detected at Ledong (low latitude environment), for the traits panicle length, grain number per branch and panicle weight, grain weight per panicle as well as branch number per panicle this factor the significant variation on individual heritability was detected at Luoyang and Gongzhuling. Several traits such as plant height, leaf number, panicle length, panicle diameter, and branch number per panicle showed higher heritability, whereas the traits including panicle weight, grain weight per panicle, and grain number per branch were detected with moderate heritability. Under three-factor combined conditions, the average heritability decreased from 0.9 to 0.7266-0.8483, and the individual heritability decreased from 0.5209-0.9931 to 0.2292-0.4263. The characters including plant height, leaf number and panicle diameter were qualified as indexes in ecological adaptability breeding in foxtail millet. The plant height, leaf number and panicle diameter positively correlated with either of panicle weight and grain weight per panicle (P < 0.001). Thus, selection for plant height, leaf number, panicle diameter and heading date might achieve the selection of panicle weight and grain weight per panicle in breeding for ecological adaptability, stable yield or high yield cultivars in foxtail millet.

Abstract:It is of great significance to evaluate the breeding and utilization value of the major QTL of important traits in maize to promote the effective development of molecular design breeding and improve the efficiency of genetic improvement of germplasm resources. In our former study, a major QTL, qPEH6.02, for plant height was identified using the introgression line 1133B (tropical maize inbred line Tzi8 as the donor parent, temperate founder inbred line B73 as the recurrent parent). In the present study, the near-isogenic introgression lines with and without qPEH6.02 were developed in the target segment by molecular marker tracking. The plant height and yield of near-isogenic introgression lines (1133BB73 and 1133BTzi8), and their hybrid crosses (crossed with both weakly heterosis inbred line of the same group and strong heterosis inbred line of the different group) were analyzed under various planting density conditions (52500 plants/hm2, 67500 plants/hm2 and 82500 plants/hm2). The plant height of 1133BTzi8 increased by 15.17-20.40 cm if compared with its near-isogenic introgression line 1133BB73 under different planting densities, whereas only increased by 3.87-5.03 cm and 3.23-5.97 cm in its weak and strong hybrid crosses, respectively. If compared with that of 1133BB73 under different planting densities, the plot yield of 1133BTzi8 was increased by >10% up to 15.00%. The plot yield in hybrids showed yield increase of >3% up to 8.85%. Collectively, these results indicate that the haplotype of qPEH6.02 from tropical maize inbred line Tzi8 has potential breeding utilization value in improving maize yield.

Abstract:Calcineurin B-like interacting protein kinase CIPK (CBL interacting protein kinases) is one of important protein kinases in the plant calcium signal pathway in response to abiotic stresses. Based on the sequence information of the CIPK family genes in Arabidopsis and rice, the members of the maize CIPK gene family were identified from the maize reference genome B73. The evolution relationship, structure variation, transcriptional profile, and transcriptional re-programing under drought stress treatments of CIPK family genes were analyzed. Forth-four maize CIPK family genes were identified and classified into five sub-families, each of which represented different characteristics on exon-intron and UTR structure. Based on the analysis of transcriptional profiles under drought stress condition, five candidate genes (ZmCIPK3, ZmCIPK7, ZmCIPK44, ZmCIPK25 and ZmCIPK28) involving into drought tolerance were identified. Furthermore, by over-expressing the ZmCIPK3 gene in Arabidopsis thaliana, under drought stress conditions the survival rate of ZmCIPK3-transgenic lines was significantly higher than that of the wild type, suggesting that ZmCIPK3 might increase the drought resistance. The activities of peroxidase (POD) and superoxide dismutase (SOD) in transgenic lines were significantly higher than those of the wild type, while the contents of malondialdehyde (MDA) and proline (Pro) were significantly lower than those of wild type. This study identified the members of the maize CIPK gene family at the genome-wide level and their transcriptional profile upon drought stress treatments, and confirmed ZmCIPK3 as a candidate gene conferring drought tolerance.

Abstract:Leaf color is usually determined by the number, structure, and photosynthetic characters of the chloroplast. Isolation of the functional genes in leaf discoloration mutants of the C4 model plant foxtail millet and deciphering their functions is a way to disclose the regulation mechanism of C4 plant chloroplast biogenesis, development and photosynthesis. In this study, a stripe-leaf mutant t122 was identified from the EMS-induced mutant library of the foxtail millet variety Yugu1. The mutant t122 was observed with developmental retardation, and irregular white stripes on leaves. In contrast to the wild type, the significant decrease on the plant height, leaf length, leaf width, main panicle diameter, main panicle weight, and seed setting rate was observed in t122 mutant, whereas an increase on the panicle number per plant was detected. The photosynthetic capacity of t122 was impaired. By the leaf anatomy analysis, no significant difference in the distance between leaf veins, the number of cell layers between vascular bundles, and the cross-sectional cell area of leaves was observed in t122; however, an increased on the leaf cell length was detected. The ultrastructural observation of chloroplasts showed that, in t122 the chloroplasts showing functional structure were only detected in subsets of leaf cells. The segregation analysis suggested that the stripe-leaf trait of t122 was controlled by a single recessive nuclei-encoding gene. Using the method of MutMap, the candidate gene was mapped to the region of 24.0 Mb - 30.0 Mb on chromosome 3. Collectively, these results laid a good foundation for future cloning and functional characterization of the stripe-leaf gene in foxtail millet.

Abstract:The heat shock protein 90 (HSP90) family members are widely involved in the growth and development of organisms as well as the transmission of stress signals. They are of significant importance in the study of signal transduction, cell cycle regulation, protein degradation and transport. In order to decipher the HSP90 gene family in foxtail millet (Setaria italica（L.）P. Beauv.), and identify their elite haplotypes being important in drought tolerance, the family members (referred SiHSP90s) were identified by taking use of the foxtail millet genome reference. Nine SiHSP90s members were identified on 5 chromosomes, with the intron number of 1 to 19, and the amino acids of deduced protein ranged from 404 to 818. Phylogenetic analysis suggested that SiHSP90s were divided into four groups. SiHSP90s were predicted to be localized in cytoplasm and endoplasmic reticulum. Based on the released foxtail millet transcriptome data, the transcriptional patterns of SiHSP90s in tissues were different. Nine stress and hormone regulatory elements were predicted via cis-acting element analysis, indicating that the transcriptional reprogramming of SiHSP90s under different abiotic stresses might be present. Haplotype analysis of 532 foxtail millet varieties showed little variation in gene region but abundant variations in the promoter region, which enables defining four haplotypes. In conjugation with phenotypic analysis, it is found that the haplotype H004 is likely the most elite haplotype showing drought tolerant, possibly due to the core sequence variations of this haplotype at cis-acting element responding to the Methyl Jasmonate (MeJA) treatments.

Abstract:In order to explore genetic loci that associated with grain number per spikelet in bread wheat (Triticum aestivum L.), a genome-wide association study was conducted using the wheat 55K genotyping assay in a diverse panel of 384 wheat genotypes. Field trials for grain number per spikelet were conducted in one location for three consecutive years. A total of 142 significant SNPs were detected for grain number per spikelet, each of which contributed the phenotypic variation from 3.27% to 6.09%. Of these, eight SNPs were detected in two or three environments. Three SNPs (AX-109986855, AX-109875224 and AX-109843323) were located on the 523.12～526.25 Mb on chromosome 2D, and the physical distance between two SNPs AX-111054388 and AX-110671159) was only 0.62 Mb on chromosome 2B. Significant differences for grain number per spikelet grouped by superior and inferior alleles in an SNP were detected (P < 0.01) across the three environments in each of these eight SNPs. For example, cultivars carrying the G/G allele at AX-109843323 on chromosome 2D resulted in an increase of 0.32, 0.37 and 0.39 grains per spikelet than that of cultivars with the C/C allele in three environments, respectively. The percentages of cultivars carrying each of the superior alleles at the eight SNPs were varied from 5.20% to 76.8%. Seven superior alleles were present with a percentage of less than 45.00% in the accessions. Furthermore, the grain number per spike in these cultivars with superior alleles (ranging from 48.45 to 53.61) among the eight SNPs were higher than that of cultivars without superior alleles (ranging from 45.04 to 47.37). Significant association in the number of favorable alleles to grain number per spikelet and grain number per spike were observed (r = 0.97 and 0.94, respectively; P < 2.0E-4). These loci associated with grain number per spikelet are useful for improving grain numbers per spike in wheat.

Abstract:Study on the morphological characteristics and genetic mechanism of wheat root system under drought stress is the basis of improving drought tolerance and stabilizing wheat yield. Genome-wide association study (GWAS) was conducted on drought resistance coefficient of wheat root traits at seedling stage, and significant correlation loci and candidate genes were identified to provide information for genetic improvement of wheat drought tolerance. In this experiment, 300 domestic and exotic excellent wheat varieties (lines) were treated by PEG-6000 to simulate drought stress at seedling stage, followed by measurement of wheat root-related phenotypic characters. Genome-wide association analysis of drought resistance coefficients of eight traits including longest root length, total root length, root surface area, root volume, root average diameter, root tip number was performed using a hybrid linear model MLM (Q+K) using 90K SNP, and candidate genes were mined for significant association loci of stable inheritance. The root traits of wheat varieties (lines) showed abundant phenotype variation under drought tolerance, with the variation coefficient of 0.17-0.58, the polymorphic information content (PIC) of 0.01-0.38, and the LD attenuation distance of 7Mb. The population structure analysis suggested three subgroups in this collection. GWAS analysis identified a total of 41 SNPS, which were significantly associated with root drought resistance traits, and mainly found on chromosomes 1B, 2B, 3A, 3B, 5A, 6B and 7B. The phenotype variation explained by a single locus ranged from 3.91% to 8.04%. Thirteen significant association loci were found in two or more traits, distributed on chromosomes 1B, 1D, 2A, 2B, 3B (2), 4A, 4D, 5A, 5B, 6B (2) and 7B, explaining 3.99%-7.05% of the phenotype variation. Tdurum_contig71499_211, Gene-1743_858 and Tdurum_contig28552_211 were significantly associated with 4-5 traits including root fresh weight, root surface area, root dry weight, root volume or root total length and root tip number. Three loci contributed to 4.12%-5.37%, 5.77%-6.70% and 4.10%-5.22% of genetic variation, respectively. Eleven candidate genes were proposed by mining 41 significant association loci of stable inheritance. With gene annotation information, TraesCS3B01G392300 (Calcium-dependent lipid-binding domain-containing protein) is known to be involved in Ca2+ level stimulation response, TraesCS1D01G036900 (Cysteine receptor-kinase protein) and TraesCS5A01G370400 (Serine protein kinase) play important roles in drought, high salt stress and various signaling processes in growth and development. TraesCS7B01G440700 (Cytochrome P450) might function in cell defense against toxic substances. These annotated genes might be used as important genes of drought tolerance in wheat.

Abstract:The panicle apical abortion (PAAB) of rice is a typical quantitative trait determined by both genotypes that interact with growth environments (i.e. the ambient temperature). A chromosome segment substitution line Ats1 (aborted top spikelet mutant 1), which was originated from the cross-combination of Qiuguang ? Qishanzhan, was used for map-based cloning of the PAAB gene ATS1. Previous linkage analysis suggested that the candidate gene of AST1 was localized on chromosome 8, sharing a long fragment of positioning interval with that of the unidentified gene qPAA8. We compared the climate differences between 2018 and other years in Beijing and the phenotype of Ats1 under different growth environment conditions. The PAAB severity of Ats1 under the high environmental temperature in 2018 was significantly alleviated compared with ordinary years, indicating that high temperature might reduce the incidence of PAAB in Ats1. In addition, through the genetic analysis to the F2 population of newly created cross-combination IRAT129?Ats1, we further found that the genetic separation of PAAB obviously deviated from ratio of the single gene dominant inheritance, i.e. 3 PAAB to 1 normal, indicating that there are additional PAAB genes involved. Here we provided a convenient strategy on developing a single gene segregating population (SGSP), based on the phenotypic analysis in combination with marker-associated selection to individuals of F2:3 lines. Finally, we finally delimited the candidate gene of ATS1 to a 57 Kb interval including four potential candidate genes, settling a foundation for the final cloning of the target gene. This method could be helpful using in fine mapping on other complex traits easily affected by environmental conditions.

Abstract:AP2/ERF transcription factor family members have been identified to play important roles in abiotic stress responses. In this study, the full-length coding sequence of the FtDREB6 gene was cloned with a length of 615 bp, which encodes for 204 amino acids residues, with a molecular weight of 22.7 kDa and an isoelectric point of 4.96 from tartary buckwheat (Fagopyrum tataricum) cultivar “Pinku 1”. The sequence of FtDREB6 represented higher homology with Arabidopsis thaliana AtERF043 by the sequence alignment on TAIR website. FtDREB6 gene was showed without the transcription activity by transactivation analysis. Moreover, by transforming the coding sequence of FtDREB6 into A. thaliana by Agrobacterium-mediated transformation approach, transgenic FtDREB6-overexpressing plants showed significant increase on the drought resistance. The expression vector containing FtDREB6 gene was transformed into Agrobacterium rhizogenes A4, which was subjected to infect explant for inducing the hairy roots. Under D-Mannitol treatment, the superoxide dismutase activity and catalase activity in overexpressing hairy roots were significantly higher than that of the control, and the content of malondialdehyde was significantly lower than the control. These results indicated that FtDREB6 was involved in responses to drought stress, which provided a reference for future deciphering the molecular mechanism for drought tolerance in tartary buckwheat.

Abstract:The nutritional and health value of peanuts has been paid more and more attention, and fresh peanuts, especially high-sugar sweet peanuts are favored by consumers. In peanut quality breeding, the sugar content of kernels has become one of the important targets, and the research on the molecular regulation mechanism of sugar metabolism is of great importance. Peanut sugar content is one of the determinants of peanut quality traits. The sugar content of the high-sugar peanut line DJ was significantly different from that of the conventional line DG. The total sugar, soluble sugar and sucrose content of DJ were 2.4 folds (p-value = 8.38×10-12 < 0.001), 2.3 folds (p-value = 3.64×10-10< 0.001) and 4.0 folds (p-value = 1.71×10-9 < 0.001) than that of DG, respectively. By RNA-seq and KEGG analysis, 3371 differentially expressed genes enriched in 117 pathways were identified, and four of them were closely related to glucose metabolism. Seven main regulation pathway related genes (including SS, FBP, HK, MAN, PFK, GPI and TPSA) and eight derivative related genes (including USP, RHM, GMLS, 2 UGDH, UGE, GLCAK and GALE) as well as a new gene GAE possibly related to sugar metabolism were detected. Out of the identified differential metabolites, sucrose, D-fructose, trehalose, D-mannose 1-phosphate, ADP-glucose, UDP-N-acetylglucosamine and uridine diphosphate glucose, three metabolites sucrose, fructose and trehalose were significantly up-regulated with the difference folds of 1.18, 1.33 and 8.37, respectively. Transcriptome and metabolome combined analysis showed that starch and sucrose metabolism and fructose and mannose metabolism were the key pathways. Sucrose, fructose and trehalose were the main differential metabolites. By qRT-PCR detection of 16 key differentially expressed genes, three genes SS, HK and GPI were up-regulated, while FBP, MAN, PFK, USP, RHM, TPSA, GMLS, 2UGDH, UGE, GLCAK, GALE and GAE were down-regulated, as revealed by the transcriptome analysis. The results of this study could provide reference for further exploring the molecular regulation mechanism of sugar metabolism in peanut.

Abstract:Homology of medicine and food is the natural endowment of adlay crops, although it was always poor palatability and not easy to cook in food processing and utilization. Seed germination was the first step of the life cycle in plants, which could be an efficient process to improve palatability and quality properties. Aiming to provide theoretical insights for guidance in adlay functional food processing and industrial utilization, the metabolomics profiles of adlay seeds in four adlay varieties ‘Xingrenbaike’, ‘Qianyi 2 hao’, ‘Anguoyiyi’ and ‘Ribenyimi’ were measured under two treatments (before and after germination), followed by statistical analysis using widely-targeted metabolomics methods to identify the differential metabolites. Of 590 metabolites detected, 190 metabolites showing statistically different were identified. After germination, compounds of lipids, organic acids, alkaloids, lignans, coumarins, phenolic acids, amino acids and derivatives, nucleotide and derivatives were up-regulated in general, while flavonoids compounds were down-regulated. The top-ten ranking up-regulated metabolic molecules were N-Phenylacetylglycine, S-Adenosylmethionine, N-α-Acetyl-L-arginine, citraconic acid, alanylleucine, Asp-phe, L-theanine, Phe-Phe, O-p-coumaroyl-O-salicyloyl quinic acid, ribulose-5-phosphate, while the top-ten ranking down-regulated molecules were proline betaine, liquiritigenin-7,4-diglucoside, avicularin, cis-Zeatin, quercetin-3-O-α-L-arabinopyranoside, chrysoeriol-7-O-glucoside, peonidin, Kaempferide, esculin hydrate and raffinose. KEGG pathway enrichments showed that the metabolism pathways including amino acids biosynthesis, aminoacyl-tRNA biosynthesis, ABC transporters, pyrimidine metabolism, zeatin biosynthesis, flavonoid metabolism, alkaloid biosynthesis, glucosinolate biosynthesis and glyceride metabolism were changed significantly. However, some bioactive molecules with physiological functions were also found with significant enrichment, such as lysoPC(18:3), Coixol, 10-Formyl-THF, oleanolic acid, gallocatechin, chlorogenic acid, syringic acid, et. Several metabolic processes involved with biosynthesis of lipids, organic acids, alkaloids, lignans, coumarins, phenolic acids, amino acids and nucleotide and their derivatives, were robust active and enhanced during germination, and some characteristic metabolites and physiologically active molecules were hunted as well.

Abstract:Hawk tea is a kind of refreshing and folk tea drink with a long drinking history in China. The primary plants used for making Hawk-tea are mainly five trees from Lauraceae family, including Litsea coreana var. lanuginosa, Machilus rehderi, Machilus Chuanchienensis, Actinodaphne cupularis, and Lindera fragrans. Whereas their studies on genetics and molecular biology remain preliminary with less supports on the exploration and utilization of these germplasm resources, which restricts the development of the Hawk-tea industry. In this study, flow cytometry and K-mer frequency analysis were performed to estimate the genome size and genomic characteristics of the five tea-like species. In flow cytometry the genomes of tomato (929 Mb) and rice (430 Mb) were used as internal control, and K-mer frequency analysis was performed using Illumina sequencing data (depth above 50X). The main results are as follows: (1) By flow cytometry, the genome size of L. coreana var. lanuginosa was 1,150.56 ± 20.47 Mb, M. rehderi was 999.83 ± 25.02 Mb, M. Chuanchienensis was 1,471.99 ± 16.31 Mb, A. cupularis was 1,123.42 ± 10.24 Mb, and t L. fragrans was 1,350.06 ± 37.28 Mb; (2) By K-mer frequency analysis, the genome size of L. coreana var. lanuginosa was 1025.91 Mb, with a heterozygosity rate of 1.29% and repetition rate of 49.98%; the genome size of M. rehderi was 1024.79 Mb, with a heterozygosity rate of 1.41% and repetition rate of 42.51%; the genome size of M. Chuanchienensis was 1234.90 Mb, with a heterozygosity rate of 1.23% and repetition rate of 50.86%; the genome size of A. cupularis was 1014.27 Mb, with a heterozygosity rate of 1.23% and repetition rate of 50.86%; the genome size of L. fragrans was 1258.00 Mb, with a heterozygosity rate of 0.74% and repetition rate of 54.89%. (3) Except for L. fragrans, four hawk-tea trees showed high heterozygous genome with medium repetitive elements. The results of this study can provide information for the genome sequencing of individual species or pan-genome research projects.

Abstract:In order to decipher the potential function of barley salt-tolerant related gene HvMBF1c and its expression pattern under salt stress treatment condition, isolation of the HvMBF1c gene via homologous cloning method was performed in two barley germplasm resources ZY26 (salt-tolerant type) and ZY218 (salt-sensitive type), followed by bioinformatics analysis of the structure, physical and chemical properties, homologous protein differences and phylogeny. HvMBF1c contains a 471bp open reading frame found on barley chromosome 7HL without intron structure, and encodes 156 amino acids. The deduced protein contains an N-terminal MBF1 domain and a C-terminal HTH domain, with the characteristics of unstable, alkaline, hydrophilic, non-transmembrane and no signal peptide structure, and its secondary structure of α helix. The phylogenetic analysis showed that HvMBF1c was highly homologous to MBF1 of various plants, and was closely related to TaMBF1c of wheat. Subcellular localization indicated that the fusion protein was mainly located in the nucleus and cytoplasm. Under NaCl stress treatment condition, the induction on the expression of the HvMBF1c gene was observed in seeds, leaves and roots at seedling stage, while the expression level in leaves was significantly higher than that in roots. The overall expression level was correlating with the ability of barley germplasm salt tolerance and the time for stress treatment. Collectively, these results demonstrated that HvMBF1c was involved in regulating the response of barley to salt stress at different growth stages.

Abstract:HIPPs (heavy metal-associated isoprenylated plant proteins) are key proteins for the safety transportation of metallic ions in the plants cell, which plays an important role in the maintenance of metal ion homeostasis and detoxification mechanism. To date, most studies on HIPPs gene family focus on model plants Oryza sativa L. and Arabidopsis thaliana L., while relatively few reports have been reported in Brassica napus L.. In this study, In this study, 104 HIPPs genes were identified in the genome of Brassica napus L. (Darmor-bzh v10) using Bioinformatics methods, which were unevenly distributed on 19 chromosomes of B. napus L.. By analyzing the physicochemical properties, we found that the amino acid number, protein molecular weight and protein hydrophobicity index of BnaHIPPs genes ranged from 120 to 630 aa, 13 827.56 to 64 467.05 Da, and -1.146 to -0.17, respectively. And the average isoelectric point was 8.07. Their expression patterns have certain spatiotemporal expression properties in different tissues and developmental periods, with the highest expression in roots. The expression pattern of BnaHIPPs were altered in response to Cd2+ stress treatment, and the relative expression levels of BnaA08p24150 and BnaA09p41730 were up-regulated in both roots and leaves. The phylogenetic relationship confirmed that 104 BnaHIPPs gene were divided into five distinct clades. In addition, collinearity analysis elucidated that during the evolution of BnaHIPPs gene famliy, most BnaHIPPs participate in the expansion of the BnaHIPPs gene family in the form of fragment replication, and only BnaC05p3800, BnaC05p3810, BnaC05p3820 and BnaC05p3830 were found to involve in the replication events of BnaHIPPs in the form of tandem repetition. Our results will lay the foundation for further research on the BnaHIPPs gene family in B. napus L..

Abstract:Sweetpotato is the seventh important food crop in the world. Although sweet potato is widely adaptable to unfavorable conditions such as drought and high salt, this species originating from tropical region remains low-temperature sensitive. In this study, cold-tolerant sweet potato variety “Liaoshu 36” was subjected for cold-stress treatments at 0 h, 6 h, 24 h and 48 h, and total RNAs were sampled for the transcriptome sequencing analysis. The results showed that 75.01 Gb transcriptome data were produced, and 76.33% of them were mapped to the reference genome. The differentially expressed gene (DEG) analysis revealed 6282 up-regulated genes were and 3881 down-regulated genes. Co-expression patterns analysis showed that 283 genes were up-regulated and 26 genes were down-regulated at all three treatments (6 h, 24 h, and 48 h). GO enrichment analysis showed that DEGs were mainly enriched on seven categories: protein kinase activity, peroxidase activity, oxidoreductase activity, protein phosphorylation, amino acid transmembrane transport, protein-chromophore linkage and pectin catabolic process. KEGG pathway enrichment showed that DEGs involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant hormone signal transduction, plant-pathogen interaction, glutathlone metabolism. Moreover, four key genes (PYL, PP2C, SnRK2 and ABF) in ABA signal transduction pathway were identified to be closely related to low temperature stress response, which provided theoretical basis for the cloning of sweet potato chilling tolerance genes and the analysis of cold tolerance mechanism.

Abstract:Soybean lipoxygenase (LOX) as an anti-nutritional factor can catalyze the enzymatic reaction of unsaturated fatty acids, resulting in an unpleasant beany taste negatively affecting the nutritional quality in soybean products. In this study, we cloned three lipoxygenase mutant genes lox1, lox2 and lox3, and analyzed their sequence variations among three genes in the near-isogenic lines (Suzuyutaka and Century) and cultivars of lipoxygenase mutant. The functional markers for LOX mutants (lox1-303 bp, lox3-266 bp, lox2-KASP, lox3-KASP) were developed and checked using agarose gel electrophoresis, capillary electrophoresis and KASP labeling techniques, followed by marker-assisted identification of their LOX genotypes in cultivars and breeding lines. Based on both of molecular marker and colorimetric methods, 25 soybean lines of LOX2 mutant (lox2) were identified. There was no significant difference in plant height, yield per plant, protein and oil content between LOX mutants and wild types within the population. Out of them, six soybean lines showing high yield and seed quality traits were identified. Collectively, this study provided the reliable functional markers and elite breeding lines in soybean molecular breeding for low beany flavor.

Abstract:The high-throughput extraction of high-quality genomic DNA is one of the basic analysis of plant molecular biology research, and an important technology for identifying genomic variation of crop germplasm resources, genetic mapping of important functional genes, crop molecular breeding based on genomic marker-assisted selection. However, the efficiency of conventional method is inadequate for large-scale DNA extraction. The automatic high-throughput instruments are expensive and consumables, and the centrifugal-sedimentation method commonly used in laboratories are tedious and involve more organic solvents. To supply the demand of high-throughput, large-scale and less expensive DNA extraction, we have developed a 96-pool magnetic separation device DNA. Using this device, the genomic DNA extraction has been succeeded for wheat, rice, maize and other cereal crops, as well as vegetable and oil crops. The integrity and purity of DNA were detected by agarose gel electrophoresis, Qubit and PCR. The results showed that (1) the plant genomic DNA had high quality and purity, good integrity; (2) one person can handle 2000 samples per day; (3) the obtained DNA samples can be used in gene cloning, transgenic plant detection, CRISPR editing site detection and NGS library construction.