YAO Yao , ZHANG Hao , WANG Xiuyun , XIA Yiping , ZHOU Hong
2025, 26(3):405-418. DOI: 10.13430/j.cnki.jpgr.20240621002
Abstract:As one of China’s ten most iconic flowers, Rhododendron is renowned for its ornamental value and cultural significance. The genus exhibits remarkable species diversity, extensive natural hybridization, and advanced horticultural development in selected varieties. However, persistent inconsistencies in varietal nomenclature have impeded international germplasm exchange. SSR markers have emerged as powerful tools for addressing these challenges, offering critical advantages in germplasm identification, genetic diversity assessment, and marker-assisted breeding. This review summarizes two decades of research progress on SSR marker applications in Rhododendron species. Approximately 509 SSR markers have been developed to date via diverse methodologies, including bioinformatics databases mining and next-generation sequencing. These markers showed cross-species transferability rate of 50% to 100% among closely related species. In terms of species conservation, SSR markers have facilitated the conservation strategy formulation, mating system analysis, and gene flow monitoring, providing empirical support for preserving genetic diversity. SSR markers are also used for authenticity identification of hybrid progeny, as well as trait-marker association studies targeting key horticultural traits such as leaf chlorosis and floral pigmentation. Finally, this review proposes future prospects of SSR markers, including development of SSR markers for endangered Rhododendron species, marker-assisted breeding for important traits, and establishment of DNA fingerprinting databases to standardize variety identification, expecting to provide references for assessment, conservation, and breeding of Rhododendron species.
HE Rui , XING Wang , LIU Dali , LU Zhenqiang
2025, 26(3):419-430. DOI: 10.13430/j.cnki.jpgr.20240624001
Abstract:Heavy metals, such as cadmium and plumbum, are increasingly contaminating soil. These pollutants not only interfere the plant life cycle but also diminish crop yields and can even lead to plant mortality. Plants have evolved a series of defense mechanisms to mitigate the stress induced by heavy metals. Plant MYB transcription factors play pivotal role as key regulators under stress conditions. They interact with downstream target genes in response to heavy metal stress, thus enhancing tolerance and minimizing damage to plants. To elucidate the molecular mechanisms by which plants cope with heavy metal stress (especially cadmium stress) is a primary goal in plant biotechnology and agricultural breeding.This article reviews several critical aspects, including the identification and characteristics of MYB family members, their functions, the mechanisms of regulating target genes, as well as exploring how MYB modulate target genes to participate in heavy metal stress response through photosynthesis and hormones. Furthermore, we discuss the adaptive mechanism of plants to heavy metal stress, where MYB transcription factors combine with target genes or promoter elements through signaling pathways, including reactive oxygen species homeostasis, abscisic acid signaling, gibberellins signaling, and photosynthesis. These interactions are critical for regulating the uptake, transport and sequestration of heavy metals in plants. Collectively, this review provides a theoretical foundation for the further exploitation and utilization of MYB transcription factors in enhancing plant resilience to heavy metal stress.
HU Liangliang , HUANG Yuning , XUE Renfeng , CHEN Tianxiao , CAO Rong , SONG Qiannan , WANG Suhua , GE Weide , WANG Lixia , CHENG Xuzhen , CHEN Honglin
2025, 26(3):431-440. DOI: 10.13430/j.cnki.jpgr.20240615001
Abstract:In response to the increasing endangerment of wild adzuki bean and its wild relatives in Liaoning province, a rescue-oriented collection effort was conducted across 36 districts (counties) in 14 cities within the province. The collected resources were evaluated for bruchid resistance. The results revealed that Vigna angularis var. nipponensis are primarily distributed in the central and eastern regions of Liaoning, especially along the eastern coastal areas, while Vigna radiata var. sublobata and Vigna minima are mainly found in the western regions. A total of 262 germplasm accessions of wild adzuki bean and its wild relatives were collected. The study highlights the severe endangerment of these species in Liaoning province, with urbanization and human activities identified as the primary drivers of this threat. Significant differences were observed between wild and cultivated adzuki bean in growth habits, stem characteristics, pod color, and seed color. Additionally, the evaluation of bruchid resistance identified two highly resistant and one resistant germplasm accessions. This is the first time that bruchid-resistant adzuki bean resources have been identified both domestically and internationally. These findings provide a critical foundation for the conservation and utilization of rare and endangered wild adzuki bean resources and its wild relatives in China and offer valuable germplasm for breeding bruchid-resistant adzuki bean cultivars.
XIN Jiajia , ZHANG Nanfeng , TU Yuqin , ZHANG Yang , GUAN Feng , TANG Jie
2025, 26(3):441-454. DOI: 10.13430/j.cnki.jpgr.20240613001
Abstract:1307 local edible bean germplasm resources in Jiangxi province, China, were investigated and analyzed. These germplasm resources are distributed across 89 counties (cities and districts) in 11 prefecture-level cities, with the highest number of resources found in Shangrao, Yichun, Ganzhou, Jiujiang, Ji'an and Fuzhou cities. The distribution quantity of edible bean germplasm resources decreases with increasing altitude. These germplasm resources belong to 7 genera and 12 species, with cowpea resources exhibiting the strongest ecological adaptability, the widest distribution area and the largest number. In addition to cowpea, mung bean, bean and adzuki bean resources are abundant in the low altitude areas, while common bean and Lima bean are more prevalent in the mid- and high-altitude areas. The higher diversity indices of edible beans in various cities are concentrated at altitudes of 0 to 500 meters. Cowpea, mung bean, rice bean and pea resources are abundant in Shangrao, Yichun, Jiujiang, Ji'an and Pingxiang cities. Cowpea and mung bean resources are abundant in Yingtan, Xinyu, Jingdezhen and Nanchang cities. Cowpea, bean and pea resources are abundant in Ganzhou city. Cowpea, rice bean and common bean resources are abundant in Fuzhou city. Through phenotypic identification, the qualitative and quantitative traits of 449 cowpea resources, which had the largest number, were analyzed. The diversity indices at the eight quality traits were ranked (grain color>tender pod color>flower color>leaf shape>pod shape>mature pod color>grain shape>growth habit). The variation coefficients of pod length and 100-seed weight were the largest among quantitative traits, indicating significant potential for improvement. Based on the comprehensive performance of agronomic traits, quality, resistance and yield, 30 elite germplasm resources were identified. These germplasm resources have great potential for further exploration and are of great significance for accelerating the innovative utilization of edible bean germplasm resources in Jiangxi province, China.
WANG Zhiqi , YAN Tingxian , YAN Xiaowen , LIANG Junchao , LE Meiwang , SUN Jian
2025, 26(3):455-469. DOI: 10.13430/j.cnki.jpgr.20240614001
Abstract:This study aimed to analyze the phenotypic diversity of sesame germplasm in Jiangxi province, China, and construct a reliable core germplasm population, providing theoretical basis and reference for promoting the efficient utilization of sesame germplasm. We used 736 sesame germplasms from various counties and cities in Jiangxi province as experimental materials, and conducted diversity analysis on 24 phenotypic traits. Three sampling methods, six sampling ratios and eight clustering methods were employed to identify optimal solution for constructing the primary core germplasm. We performed mean T-test and variance F-test on multiple parameters of the original germplasm and core germplasm, and compared the eigenvalues, contribution rates, and cumulative contribution rates of the two populations through principal component analysis. In addition, we obtained genotype data for 64 germplasms and 16 core germplasms of Ji′an using 12 pairs of polymorphic markers, followed by polymorphism analysis, evaluation, and genetic similarity analysis. The 736 local sesame germplasms in Jiangxi province exhibited rich genetic diversity. The genetic diversity index of phenotypic traits ranged from 0.5129 to 2.0833, with a variation range of 4.83% to 41.52%. The genetic diversity index of quantitative traits (1.7140 to 2.0833) was generally higher than that of qualitative traits (0.5129 to 1.1054). The 110 core germplasm constructed using the “multiple clustering priority sampling method + 15% sampling ratio + variable class average method + Euclidean distance” effectively represented the diversity of the original collection. The cumulative contribution rates of the original collection and core collection were 80.533% and 82.631%, respectively, indicating that the core collection could explain over 80% of the genetic information. Molecular analysis of the sample showed, 96.25% of the polymorphic loci in 16 core germplasms were in included in 64 original germplasms, both were essentially similar on polymorphisms, with no significant difference in the mean T-test (except for the number of observed alleles). The genetic similarity between the two collections was also essentially similar. The 16 mini-core germplasms could preliminarily represent the genetic diversity of the 64 Ji′an sesame germplasms. Collectively, these results indicated that the 110 core germplasm collection could represent the genetic diversity of the 736 Jiangxi sesame germplasms to a significant extent for preservation and utilization.
WANG Shizhuang , NIE Yamin , HUANG Jingfen , ZHANG Qiaoling , ZHENG Chongke , XIE Xianzhi , WANG Yanyan , XING Meng , CHEN Wenxi , CHEN Ziyi , ZHENG Xiaoming , WANG Wensheng , YANG Qingwen , QIAO Weihua
2025, 26(3):470-480. DOI: 10.13430/j.cnki.jpgr.20240602001
Abstract:Rice is a salt-sensitive plant, and soil salinization significantly impacts rice performance. Therefore, exploring excellent haplotypes of salt-tolerant genes and generating elite germplasm are of great significance for rice breeding. In this study, we firstly analyzed 236 core germplasm lines collected from the 3K Rice Genome Project Database, for salt tolerance during the seedling stage and throughout the entire growth period in the field. A highly salt-tolerant germplasm ‘71011’ from Australia was identified. This germplasm survived for 25.5 d and exhibited a salt tolerance level of 5.2 under 150 mmol/L NaCl treatment conditions, with a 100% survival rate under 0.3% to 0.5% salt treatment in the paddy field. We further conducted haplotype analysis on 20 reported salt tolerance genes in the core collection. Eight genes, including AKT1, CPK12, MYB48, P5CS1, SIK1, SKC1, SNAC1, and HKT1, were identified as having haplotypes associated with salt tolerance. One salt-tolerant variety ‘Yanfeng 47’ and one normal variety ‘Nongken 57’ were selected as parents to generate recombinant inbred lines. Finally, three molecular markers, which have been confirmed by PCR and qRT-PCR, were designed for selecting elite haplotypes of three genes, AKT1, MYB48, and HKT1. Through marker-assisted selection, we successfully developed three high salt-tolerance lines by aggregating these elite haplotypes. Our results provide available germplasm resources, molecular markers and innovative lines for breeding new salt-tolerant rice varieties.
JIN Jinghua , LI Shufang , ZHAO Yadong , WANG Di , ZHANG Yu , JIN Guoguang , LI Henan , QUAN Chengzhe , ZHANG Qiang
2025, 26(3):481-495. DOI: 10.13430/j.cnki.jpgr.20240602002
Abstract:Rice germplasm resources are important foundation for rice genetic improvement and new variety breeding. The study of genetic diversity of rice germplasm resources plays an important role in broadening the genetic background of rice. In this study, genetic diversity analysis of 20 important agronomic traits of 1775 rice germplasm resources was carried out using multiple analysis methods.The results showed that the variation coefficients of agronomic traits varied considerably, ranging from 4.42% (grain thickness) to 89.75% (empty seed), and empty seed had richer genetic variation. And the changes in the genetic diversity index ranged from 1.585 (empty seed)~2.069 (heading date), with richer diversity in heading date. Through the separate analysis of germplasm from 11 provinces (cities),it was found that the germplasm from Jilin province had richer diversity in seven traits such as panicles per plant and spikelets per panicle;the germplasm from Yunnan province had richer diversity in four traits such as first heading date and panicle length; and the germplasm from Heilongjiang province had richer diversity in three traits such as heading date.The results of different types of germplasm showed that 11 traits were more abundant in landrace, such as flag leaf length and plant height; and the 9 traits were more abundant in advanced cultivar, such as growth stage traits and panicles per plant .The correlation analysis showed that 149 correlation coefficients reached the highly significant level (P<0.01), among which three growth stage traits had highly correlated with other agronomic traits , for example first heading date. Principal component analysis revealed that the first six principal components had a cumulative contribution of 79.309% and the trait related to growth stage had the highest contribution.Through cluster analysis,1775 rice germplasm were classified into three clusters. The germplasm from the three northeastern provinces as well as Beijing and Hangzhou was cluster I.The germplasm in this cluster was richer in genetic diversity for 10 traits, such as first heading date, tillering number, and panicles per plant, which can provide excellent germplasm for innovation of rice germplasm resources and the selection and breeding of new varieties in the future. ClusterⅡ contains only Ningxia germplasm, which indicates that the germplasm resources of Ningxia are distantly related to those of other provinces (cities), and can play an important role in broadening the genetic base of rice germplasm resources in the future. Cluster III contains Hebei, Shandong, Yunnan, Jiangsu and Xinjiang germplasm. The genetic diversity of grain length in this cluster is more abundant, which can provide abundant germplasm for rice quality breeding in the future.
JIANG Chuan , ZHU Yebao , CHEN Lizhe , LI Qinghua , ZHANG Haifeng , WANG Jinying
2025, 26(3):496-506. DOI: 10.13430/j.cnki.jpgr.20240924001
Abstract:The data on main agronomic traits, blast resistance, and rice quality of certified rice varieties in Fujian province from 2000 to 2023 were extracted from the certification announcements of the National Rice Data Center for statistical analysis. The results help to reveal the evolutionary trends of these traits and the distribution frequency of certified rice varieties in different years, and provide insights for developing new rice breeding in the future in Fujian province. The results showed that a total of 609 rice varieties were certified in Fujian province in the past 24 years. They were classified into 593 indica rice, 14 indica-japonica hybrids, 2 japonica rice by the subspecies, and 580 hybrid rice,29 conventional rice by breeding method. The varieties bred and planted in Fujian were mainly indica rice. In Fujian province, three-line hybrid rice breeding is the strong point. The yields of these rice varieties mainly ranged from 450 to 650 kg/667 m2, and appeared a general upward trend with the increase of years. The inter-annual trends of four yield components were as follows: in 2000-2013, the number of fertile panicles per unit area presented a downward trend, while spikelets per panicle and 1000-grain weight showed a general upward trend; but in 2014-2023, the number of fertile panicles per unit area, spikelets per panicle, 1000-grain weight remained stable in general; the seed setting rate fluctuated between years. Grain yield showed significantly positively correlated with panicle length, spikelets per panicle, seed setting rate, and 1000-grain weight, but had significantly negatively correlated with the number of fertile panicles per unit area. Among these 609 rice varieties, 228 varieties showed moderate to high resistant to blast, and 310 varieties were high quality rice. The six traits of rice quality displayed a fluctuating state with years. The certified rice varieties in 2019-2023 showed an upward trends of whole milled rice rate, alkali digestibility value, and gel consistency, and a downward trend of chalkiness, transparence, and a stable trend of amylose content, and a gradually increase of the rate of achieving high-quality rice standards.
ZHAO Juanying , LI Jinbiao , LI Haoxiang , WANG Huiyan , ZHANG Xiaojuan , FAN Xinqi , LIANG Du , GUO Qi , LIU Qingshan , ZHANG Yizhong
2025, 26(3):507-518. DOI: 10.13430/j.cnki.jpgr.20240621001
Abstract:Brassinosteroids (BRs) are class of important hormones in plants, which play a role in regulating plant growth and development and resisting various environmental stresses. BZR transcription factors are key regulatory factors in the BRs signaling pathway and transmit BRs signals by regulating the expression of target genes. To further study the biological characteristics and functions of BZR genes in sorghum, this study identified 10 BZR genes from the sorghum genome. The tissue-specific expression analysis showed that SbBZR3, SbBZR4, and SbBZR10 are highly expressed in multiple tissues as well as have high expression levels during the grain development process. Meanwhile, based on the resequencing results and grain phenotype data of 340 sorghum germplasm resources, the superior alleles of SbBZRs were identified. The results showed that the superior alleles SbBZR3-SNP404 (T) was significantly associated with grain length, and SbBZR10-SNP660 (A) was significantly associated with grain length, grain width and 1000-grain weight. Both SbBZR3-SNP404 (T) and SbBZR10-SNP660 (A) were artificially selected during the evolutionary process. This study not only lays a foundation for revealing the action mechanism of BZR genes in sorghum, but also provides a reference for using excellent alleles to improve grain size and promote the creation of new sorghum seeds with high yield.
CUI Yongmei , LI Jie , ZHANG Li , YAO Youhua , YAO Xiaohua , WU Kunlun
2025, 26(3):519-529. DOI: 10.13430/j.cnki.jpgr.20240619001
Abstract:Drought is one of significant environmental stresses in the Tibetan Plateau region. Breeding drought-tolerant varieties in Qingke (Tibetan hulless barley) is an effective strategy to enhance its drought resistance. In this study, we evaluated the drought resistance of 246 Qingke germplasm resources at both the seedling and reproductive stages. The drought resistance was classified by measuring relative electrolyte leakage at the seedling stage, and at the reproductive stage, plant height (PH), spike length (SL), kernels per ear (KN), and thousand grain weight (TGW) were measured and analyzed. A comprehensive evaluation model (D-value) was developed to identify suitable evaluation indices for drought resistance. The results showed that drought stress resulted in a significant decrease of 5.39% to 18.87% in the four drought-related traits at the reproductive stage, with spike length being the most sensitive and significantly correlated with drought resistance. The coefficients of variation of these traits ranged from 11.98% to 24.96%, highlighting substantial variation in drought resistance among the germplasms. Specifically at the seedling and reproductive stages, 21 and 36 were identified as highly-resistant/resistant accessions, respectively, and 84 and 71 were identified as highly-sensitive/sensitive accessions, respectively. When combining the results from both stages, three accessions showed highly-resistant/resistant, and 26 accessions showed highly-sensitive/sensitive. However, there was no significant correlation between relative electrolyte leakage and the comprehensive evaluation D-value. Collectively, this study provides valuable germplasm resources for future breeding programs and deciphering the drought-tolerance mechanisms during critical growth periods of Qingke.
2025, 26(3):530-538. DOI: 10.13430/j.cnki.jpgr.20240619002
Abstract:In order to provide reference for the protect, development and utilization of Vaccinium bracteatum resources, a total of 70 germplasm resources from 5 geographical populations were genotyped by GBS (Genotyping-by-Sequencing) technique to develop SNP markers. Using the developed markers, we investigated the genetic diversity and population genetic structure of V. bracteatum. The result shows a total of 9752 highly consistent and effective SNP markers were obtained through sequencing data analysis. 5 geographical populations of V. bracteatum all have high levels of genetic diversity, with an average effective number of alleles (Ne) of 1.523, expected heterozygosity (He) of 0.219, and observed heterozygosity (Ho) of 0.231. Among the 5 populations, the Liyang population had the highest genetic diversity. Analysis of variance for molecular variation(AMOVA) revealed that 64.45% of the total genetic variation resided among individuals. The fixation index (Fst) showed a high degree of genetic differentiation among the 5 geographical populations, with the highest Fst values(0.406) observed between the Liyang and Shangyou populations. Based on the results of NJ Phylogenetic tree, V. bracteatum resources clustered into three branches, which did not show obvious correspondence between geographical location and genetic relationships. The STRUCTURE analysis clustered the V. bracteatum resources into three subgroups, the results of principal component analysis was consistent with it, and different geographical populations are distributed in each subgroup, indicating the existence of high gene exchange in V. bracteatum resources. This study provides reference for selection and breeding of V. bracteatum and germplasm conservation.
WANG Bijun , ZHANG Qiuping , LIU Weisheng , LIU Shuo , LIU Ning , ZHANG Yuping , ZHANG Yujun , XU Ming , MA Xiaoxue , LIU Jiacheng , ZHAO Haijuan
2025, 26(3):539-553. DOI: 10.13430/j.cnki.jpgr.20240616001
Abstract:To explore the genetic diversity of apricot leaf morphology and facilitate the collection of apricot germplasm resources and variety identification, this study investigated 28 leaf phenotypic traits across 142 germplasm resources. Leaf morphological characteristics were rapidly evaluated using picture recognition technology. The results of phenotypic trait diversity analysis showed the coefficients of variation (CV) of the 13 qualitative and 8 quantitative traits were higher than 10%, indicating rich genetic diversity on leaf morphology in the collection. Correlation analysis revealed highly significant positive correlations among leaf area, leaf perimeter, leaf length, and leaf width; highly significant negative correlations between leaf base shape, leaf base angle, and leaf length/width; and significant negative correlations between leaf roundness and leaf tip length. Principal component analysis indicated that the first principal component, consisting of leaf area, leaf circumference, leaf length, leaf width, and petiole length, mainly reflected traits related to leaf blade size. The second principal component reflected traits related to leaf blade color, while the third and fourth principal components reflected traits related to leaf blade shape and blade sawtooth height, respectively. Cluster analysis broadly classified these samples into eight taxa, including large-leafed-cuneate, small-leafed-light green, large-leafed-dark green, small-leafed-dark green, small-leafed-rounded, large-leafed-cordate, large-leafed-truncate, and mixed taxa, and the Ⅷ taxon was divided into six subgroups. Collectively, this study suggested three qualitative traits, leaf tip length, leaf margin sawtooth depth, and widest position of the leaf, to identify different apricot varieties, thus providing a reference for future evaluations of leaf morphology and variety recognition of apricot germplasm resources in China.
ZHANG Xinfang , ZHANG Shuhang , LI Ying , GUO Yan , LIU Jinyu , FAN Liying , WANG Guangpeng
2025, 26(3):554-565. DOI: 10.13430/j.cnki.jpgr.20240620004
Abstract:The purpose of this study was to explore the phenotypic diversity of Castanea mollissima Bl. in Yanshan Mountains, and evaluate the nut appearance and economic traits targetedly using a variety of analytical methods. The phenotypic datasets (11 descriptive traits and 15 numerical traits) in 118 chestnut variety resources in Yanshan Mountains were collected. The Shannon-Wiener diversity index, principal component analysis, membership function and cluster analysis were used to evaluate and guide the appropriate utilization methods according to the nut phenotypic characteristics. The value of Shannon-Wiener diversity index(H')of 11 descriptive traits ranged from 0.33 (number of pubescence) to 1.14 (color of nut), and the value of coefficient of variation was 11.63% (obviousness of stripes) - 51.07% (wiring shape). The value of coefficient of variation of 15 numerical traits ranged from 3.09% (kernel rate) to 24.69% (shell weight), and the value of coefficient of variation of shell weight, bar size, kernel weight and nut size was greater than 20%. The Shannon-Wiener diversity index ranged from 1.85 (base width) to 2.09 (nut length). There were significant or extremely significant correlations among most numerical traits. The results of principal component analysis showed that the cumulative contribution rate of the first four principal components was 80.768%, and contribution ratio of the first principal component was the largest, which could be used as a comprehensive index related to nut size. The variety resources with higher comprehensive scores of nut processing economic traits included Jianli, Nanchui 5, Xinglong 1, Maxingli, Yanli 1, Dabanhong, Yanli, Pingquan (Ge), Funingbaopi and Timashisheng.
ZHENG Yongjie , ZHANG Yueting , LIU Xinliang , TU Bailian , Wu Yanfang
2025, 26(3):566-574. DOI: 10.13430/j.cnki.jpgr.20240618001
Abstract:Phoebe chekiangensis is a rare and endangered species in China, and investigating its genetic diversity and genetic structure of populations provides a scientific basis for the effective protection and utilization. In this study, 15 pairs of SSR markers were used to analyze 175 germplasm resources from 10 populations by capillary electrophoresis. A total of 114 alleles (Na) were detected, with an average of 2.371 effective alleles (Ne) per primer pair. The polymorphic information content (PIC) of the SSR primers ranged from 0.323 to 0.844, averaging 0.629. The populations exhibited a moderate degree of genetic diversity (Ho=0.621, He=0.478). The inbreeding coefficient within subpopulations (Fis) was -0.237, while the inbreeding coefficient for total population (Fit) was 0.082, indicating a high rate of heterozygosity. There was substantial genetic differentiation (Fst=0.275) and limited gene flow (Nm=0.763) among populations. Analysis of molecular variance (AMOVA) showed that inter-individual differences within populations accounted for 78.7% of the total variation (P<0.001). Population structure and cluster analysis divided the 10 populations from different provenances into three groups, with some evidence of gene introgression between populations. Habitat fragmentation and human disturbance are likely the primary reasons of endangerment for P. chekiangensis. To protect its genetic diversity of P. chekiangensis, measures by combining in situ conservation and ex situ conservation should be implemented.
JIAO Yun , GAO Zhongshan , WANG Guoyun , CHEN Fangyong , YAO Xiaoying , ZHOU Chaochao
2025, 26(3):575-588. DOI: 10.13430/j.cnki.jpgr.20240626001
Abstract:The InDel markers have been extensively used in molecular marker-assisted breeding for fruit trees. However, limited studies have been conducted on their application in Chinese bayberry (Morella rubra), a traditional Chinese fruit tree. This study identified 25831 InDels, ranging from 1 to 50 bp in size, through whole-genome resequencing and bioinformatics analysis of 103 Chinese bayberry core germplasm accessions. The frequency of InDel variation across different chromosomes ranged from 1/11297 to 1/8903, with chromosome CM025856.1 exhibiting the highese frequency of InDel mutation. Annotation analysis showed that 1312 InDels were located in gene exon regions, while 21055 and 6659 InDels were distributed in the intergenic and intron regions, respectively. Gene Ontology (GO) analysis indicated that these InDels were primarily associated with for cellular processes and metabolic processes in biological processes, and with binding and catalytic activity in molecular functions. KEGG pathway analysis demonstrated that the InDel-containing genes were predominantly involved in secondary metabolism, carbon metabolism and nucleocytoplasmic transport. Genome-wide association analysis identified 20 InDels significantly associated with fruit maturity traits. Functional annotations of these InDels revealed associations with mitochondrial and plastid structural genes, riboside triphosphate hydrolase, and cytokinin signaling proteins. Further validation and analysis identified the InDel EP-18 marker as having the highest accuracy (89.25%) for identifying fruit maturity traits. Gene prediction analysis indicated that this locus encodes an early nodulin family gene. In conclusion, the InDel EP-18 marker identified in this study provides an important theoretical basis for molecular assisted breeding of Chinese bayberry.
CHENG Xinqi , WU Shiying , LI Xinyue , LIU Wenchao , LIU Hongtao , HU Xiaoming , ZHU Huaguo
2025, 26(3):589-601. DOI: 10.13430/j.cnki.jpgr.20240619003
Abstract:To explore the key genes involved in oil content and fatty acid metabolism in Camellia oleifera, transcriptome analysis was performed on the kernel at three key developmental stages. Correlation analysis was conducted on the expression levels, oil content, and proportions of each fatty acid component of the enriched fatty acid metabolism key genes. Transcriptome analysis revealed 17772 differentially expressed genes (DEGs), of which 11006 were up-regulated, and 6766 were down-regulated. Gene Ontology (GO) analysis showed that 1302 DEGs were enriched with 195 GO terms across the three comparative groups. DEGs in each pairwise group were enriched with 14, 1, and 17 GO terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs were enriched in five pathways: flavonoid biosynthesis, phenylpropanoid biosynthesis, diarylheptanoid and gingerol biosynthesis, and glutathione metabolism. During the critical period of fatty acid synthesis, in the Em0707vsEm1003 comparison group, DEGs were enriched in four pathways: fatty acid biosynthesis, fatty acid metabolism, biotin metabolism and pyruvate metabolism. Twelve DEGs were involved in the fatty acid metabolism pathway. Further determination of oil content and fatty acid composition at different stages of kernel development and correlation analysis, showed that the expression levels of ACC, KASIII, PATE, KAT2 and SAD genes were extremly significantly positively correlated with seed oil content and oleic acid. In contrast, KASIII, ACC, PATE, and KAT2 genes were extremly significantly negatively correlated with palmitic acid. These genes may be key regulators of oil content and fatty acid metabolism in Camellia oleifera, thus providing a scientific basis for future genetic improvement of Camellia oleifera.
ZHANG Xiang , HAN Jianan , YU Lili , ZHOU Ya , WANG Xiaobo , QIU Lijuan
2025, 26(3):602-610. DOI: 10.13430/j.cnki.jpgr.20240604001
Abstract:The photoperiod sensitivity of soybean limits the popularization of excellent soybean varieties for planting. In this study, we created new soybean varieties with early maturity and stable yield by reducing the sensitivity of soybean to photoperiod and expanding the planting range of good varieties. Three soybean GmphyA2 pure mutants were obtained using CRISPR/Cas9 technology. The created GmphyA2 mutants encodes a truncated protein without PHY structural domain due to a base deletion resulting in a code-shift mutation. Comparisons were made to characterize the fertility, plant size, and yield of the GmphyA2 mutant and the WT ‘Jack’. The results showed that because of significantly increased expression of GmFT2a and GmFT5a during the pre-flowering period, the GmphyA2 mutant flowered 5-6 d earlier and matured 6-11 d earlier compared with the WT. Although the fertility period was shortened, grains weight per plant was not significantly different from that of the WT due to a significant increase in both the effective number of branches and the number of grains per plant in the GmphyA2 mutant. These results indicate that the editing of GmphyA2 using CRISPR/Cas9 technology has created a new soybean germplasm with unchanged yield per plant with shortened fertility period, which provides a new genetic resource for breeding for early maturity and high yield.