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Genome-Wide Analysis for Yield-Related Agronomic and Biochemical Traits of Chinese and Bangladeshi Grass Pea Genotypes Using ssr markers

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Phyton-International Journal of Experimental Botany 2024年第8期93卷 1781-1804页

作者： Md.Mosiur Rahman Md.Ruhul Quddus Quanle Xu Muhammad Malek Hossain Rong Liu Mengwei Li Xin Yan Guan Li Yishan Ji Chenyu Wang Ashutosh Sarker Tao Yang Xuxiao Zong Md.Monoar Hossain Saleh Alfarraj Mohammad Javed Ansari Sagar Maitra Akbar Hossain Institute of Crop Sciences Chinese Academy of Agricultural Sciences(CAAS)Beijing100081China Pulses Research Center Bangladesh Agricultural Research Institute(BARI)Gazipur1701Bangladesh Hybrid Rice Division Bangladesh Rice Research Institute(BRRI)Gazipur1701Bangladesh Northwest Agriculture&Forestry University Yangling712199China International Center for Agricultural Research in the Dry Areas(ICARDA) New Delhi110012India Wheat Breeding Division Bangladesh Wheat and Maize Research InstituteDinajpur5200Bangladesh Zoology Department College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia Department of Botany Hindu College Moradabad(Mahatma Jyotiba Phule Rohilkhand UniversityBareilly)Moradabad244001India Department of Agronomy and Agroforestry Centurion University of Technology and ManagementOdisha761211India Soil Science Division Bangladesh Wheat and Maize Research InstituteDinajpur5200Bangladesh

Grass pea(Lathyrus sativus L.)is an imperative food crop cultured in dryland agricultural *** is a vital source of dietary protein to millions of populaces living in low-income countries in South-East Asia and *** study highlights the improvement of genomic properties and their application in marker-trait relationships for 17 yield-related characters in 400 grass pea genotypes from China and *** characters were assessed via 56 polymorphic markers using general linear model(GLM)(P+G+Q)and mixed linear model(MLM)(P+G+Q+K)in the tassel software based on the linkage disequilibrium and population structure *** structure analysis showed two major groups and one admixed group in the *** significant loci pairs of linkage disequilibrium(LD)mean value(D′)was 0.479.A total of 99 and 61 marker-trait associations in GLM and MLM models allied to the 17 traits were accepted at a 5%level of *** these markers,21 markers were associated with more than one trait;12 marker-trait associations passed the Bonferroni correction *** models found six markers C41936,C39067,C34100,C47146,C47638,and C43047 significantly associated with days to maturity,flower color,plant height,and seed per pod were detected in the Hebei and Liaoyang location(p≤0.01),and the interpretation rate(R^(2)value)11.2%to 43.6%.Conferring to the consequences,the association analysis methodology may operative system for quantitative,qualitative,and biochemical traits related to gene position mapping and support breeders in improving novel approaches for advancing the grass pea quality.

关键词： Grass pea dryland agriculture genome-wide association yield contributing traits ssr markers

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ssr markers development and their application in genetic diversity evaluation of garlic(Allium sativum)germplasm

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Plant Diversity 2022年第5期44卷 481-491页

作者： Xiaxia Li Lijun Qiao Birong Chen Yujie Zheng Chengchen Zhi Siyu Zhang Yupeng Pan Zhihui Cheng College of Horticulture Northwest A&F UniversityYangling712100Shaanxi ProvinceChina

Garlic(Allium sativum),an asexually propagated vegetable and medicinal crop,has abundant genetic *** diversity evaluation based on molecular markers has apparent advantages since their genomic abundance,environment insensitivity,and non-tissue specific ***,the limited number of available DNA markers,especially ssr markers,are insufficient to conduct related genetic diversity assessment studies in *** this study,4372 EST-ssr markers were newly developed,and 12 polymorphic markers together with other 17 garlic ssr markers were used to assess the genetic diversity and population structure of 127 garlic *** averaged polymorphism information content(PIC)of these 29 ssr markers was 0.36,ranging from 0.22 to ***-nine polymorphic loci were detected among these accessions,with an average of 3.48 polymorphic loci per *** the clustering analyses based on either the genotype data of ssr markers or the phenotypic data of morphological traits obtained genetic distance divided the 127 garlic accessions into three ***,the Mantel test showed that genetic distance had no significant correlations with geographic distance,and weak correlations were found between genetic distance and the phenotypic *** analysis showed that the main genetic variation of this garlic germplasm collection existed in the within-population or *** of this study will be of great value for the genetic/breeding studies in garlic and enhance the utilization of these garlic germplasms.

关键词： Garlic ssr markers Genetic diversity Population structure

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Bulked Segregant Analysis to Detect QTL Related to Heat Tolerance in Rice(Oryza sativa L.) Using ssr markers

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Agricultural Sciences in China 2009年第4期8卷 482-487页

作者： ZHANG Gui-lian CHEN Li-yun XIAO Guo-ying XIAO Ying-hui CHEN Xin-bo ZHANG Shun-tang Department of Agronomy Hunan Agricultural University Changsha 410128 P.R.China Institute of Subtropical Agriculture Chinese Academy of Sciences Changsha 410125 P.R.China Laboratory of Gene Engineering Hunan Agricultural University Changsha 410128 P.R. China

The study was undertaken to assess the genetic effect of quantitative trait loci （QTLs） conferring heat tolerance at flowering stage in rice. A population consisting of 279 F2 individuals from the cross between 996, a heat tolerant cultivar and 4628, a heat-sensitive cultivar, was analyzed for their segregation pattern of the difference of seed set rate under optimal temperature condition and high temperature condition. The difference of seed set rate under optimal temperature condition and high temperature condition showed normal distribution, indicating the polygenic control over the trait. To identify main effect of QTL for heat tolerance, the parents were surveyed with 200 primer pairs of simple sequence repeats （ssr）. The parental survey revealed 30% polymorphism between parents. In order to detect the main QTL association with heat tolerance, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The association of putative markers identified based on DNA pooling from selected segregants was established by single marker analysis （SMA）. The results of SMA revealed that ssr markers, RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively, accounted for 17 and 3% of the total variation respectively. The heat tolerance during flowering stage in rice was controlled by multiple gene. The ssr markers, RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively, accounted for 17 and 3% of the total variation respectively. The two genetic loci, especially for RM3735 on chromosome 4, can be used in marker-assistant-selected method in heat tolerance breeding in rice.

关键词： bulked segregant analysis heat tolerance QTL rice (Oryza sativa L.) ssr markers

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Association analysis of grain traits with ssr markers between Aegilops tauschii and hexaploid wheat(Triticum aestivum L.)

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Journal of Integrative Agriculture 2015年第10期14卷 1936-1948页

作者： ZHAO Jing-lan WANG Hong-wei ZHANG Xiao-cun DU Xu-ye LI An-fei KONG Ling-rang State Key Laboratory of Crop Biology College of Agronomy Shandong Agricultural University Taishan Polytechnic

Seven important grain traits, including grain length（GL）, grain width（GW）, grain perimeter（GP）, grain area（GA）, grain length/width ratio（GLW）, roundness（GR）, and thousand-grain weight（TGW）, were analyzed using a set of 139 simple sequence repeat（ssr） markers in 130 hexaploid wheat varieties and 193 Aegilops tauschii accessions worldwide. In total, 1 612 alleles in Ae. tauschii and 1 360 alleles in hexaploid wheat（Triticum aestivum L.） were detected throughout the D genome. 197 marker-trait associations in Ae. tauschii were identified with 58 different ssr loci in 3 environments, and the average phenotypic variation value（R2） ranged from 0.68 to 15.12%. In contrast, 208 marker-trait associations were identified in wheat with 66 different ssr markers in 4 environments and the average phenotypic R2 ranged from 0.90 to 19.92%. Further analysis indicated that there are 6 common ssr loci present in both Ae. tauschii and hexaploid wheat, which are significantly associated with the 5 investigated grain traits（i.e., GA, GP, GR, GL, and TGW） and in total, 16 alleles derived from the 6 aforementioned ssr loci were shared by Ae. tauschii and hexaploid wheat. These preliminary data suggest the existence of common alleles may explain the evolutionary process and the selection between Ae. tauschii and hexaploid wheat. Furthermore, the genetic differentiation of grain shape and thousand-grain weight were observed in the evolutionary developmental process from Ae. tauschii to hexaploid wheat.

关键词： association analysis grain traits Aegilops tauschii Triticum aestivum ssr markers

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Assessment of wheat variety distinctness using ssr markers

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Journal of Integrative Agriculture 2015年第10期14卷 1923-1935页

作者： WANG Li-xin QIU Jun CHANG Li-fang LIU Li-hua LI Hong-bo PANG Bin-shuang ZHAO Chang-ping Beijing Engineering and Technique Research Center for Hybrid Wheat Beijing Academy of Agricultural and Forestry Sciences National Agriculture Technology Extension and Service Center Ministry of Agriculture National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science Chinese Academy of Agricultural Sciences

Assessment of variety distinctness is important for both the registration and the protection of particular variety. However, the current testing system, which assesses a range of morphological characters of each pair of varieties grown side-by-side, is time-consuming and is not suitable for the assessment of hundreds of samples. The objective of this study was to develop a procedure for the assessment of wheat variety distinctness using simple sequence repeat（ssr） markers. A comparison between the molecular and morphological profile of 797 varieties was made. On the basis of the comparison, pairs of varieties with a genetic similarity value（GSV） ≤90% were deemed to be distinct, accounting for ~85% of varieties assessed in wheat regional trials. For the remaining ~15% of varieties, GSVs between different varieties were 〉90%, among which ~35% were not distinct and the other ~65% were distinct. Therefore, if given a GSV〉90%, the pairs of varieties should be morphologically assessed in the field. To avoid any errors in the assessments, we proposed the elimination of contaminant plants from the sample before comparing the varietal genotypes, scoring of the genotype at each locus with a pair of allele numbers when constructing a molecular profile, and faithfully recording two alleles at a non-homozygous locus. To reduce the workload and cost, a three-grade markers comparison among varieties is suggested. In addition, 80 ssr markers and a technical procedure for assessment of wheat variety distinctness have been proposed. Based on the procedure, the distinctness assessment of ~85% of all wheat varieties is completed in our laboratory annually. Consequently, total field assessment has been reduced considerably.

关键词： wheat variety distinctness assessment ssr markers

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Fingerprinting 146 Chinese chestnut(Castanea mollissima Blume)accessions and selecting a core collection using ssr markers

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Journal of Integrative Agriculture 2021年第5期20卷 1277-1286页

作者： NIE Xing-hua WANG Ze-hua LIU Ning-wei SONG Li YAN Bo-qian XING Yu ZHANG Qing FANG Ke-feng ZHAO Yong-lian CHEN Xin WANG Guang-peng QIN Ling CAO Qing-qin Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing University of AgricultureBeijing 102206P.R.China College of Plant Science and Technology Beijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing 102206P.R.China College of Landscape Architecture Beijing University of AgricultureBeijing 102206P.R.China Chestnut Technology Experiment and Extension Station of Huairou District Beijing 102206P.R.China Shandong Institute of Pomology Shandong Academy of Agricultural SciencesTai’an 271000P.R.China Changli Institute of Pomology Hebei Academy of Agriculture and Forestry SciencesChangli 066600P.R.China

Chinese chestnut is an important nut tree around the *** the types of Chinese chestnut resources are abundant,resource utilization and protection of chestnut accessions are still very ***,we fingerprinted and determined the genetic relationships and core collections of Chinese chestnuts using 18 fluorescently labeled ssr markers generated from 146 chestnut *** analyses showed that these markers from the tested accessions are highly polymorphic,with an average allele number(N_(a))and polymorphic information content(PIC)of 8.100 and 0.622 per locus,*** these strongly distinguishing markers,we successfully constructed unique fingerprints for 146 chestnut accessions and selected seven of the ssr markers as core markers to rapidly distinguish different *** exploration of the genetic relationships among the five cultivar groups indicated that Chinese chestnut accessions are divided into three regional type groups:group I(North China(NC)and Northwest China(NWC)cultivar groups),group II(middle and lower reaches of the Yangtze River(MLY)cultivar group)and group III(Southeast China(SEC)and Southwest China(SWC)cultivar groups).Finally,we selected 45 core collection members which represent the most genetic diversity of Chinese chestnut *** study provides valuable information for identifying chestnut accessions and understanding the phylogenetic relationships among cultivar groups,which can serve as the basis for efficient breeding in the future.

关键词： Castanea mollissima ssr markers fingerprinting phylogeny core collections

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Construction of a genetic map and localization of QTLs for yield traits in tomato by ssr markers

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Progress in Natural Science:Materials International 2005年第9期15卷 793-797页

作者： LIU Yang 1,2 , CHEN Huoying1**, WEI Yutang2 and ZHUANG Tianming1(1. Department of Plant Science, Shanghai Jiaotong University, Shanghai 201101, China 2. Department of Horticulture, Shenyang Agricultural University, Shenyang 110161, China) Department of Plant Science Shanghai Jiaotong University Shanghai 201101 China. Department of Horticulture Shenyang Agricultural University Shenyang 110161 China

Using an F2population derived from the hybrid of Lycopersicon esculentum Mill. ‘XF 98-7’× Lycopersicon pimpinellifolium LA2184, a ssr genetic linkage map of tomato is constructed. The map contains 112 markers and spans 808.4 cM with an average distance of 7.22 cM between loci. Two quantitative trait loci （QTLs） for first flower node on chromosomes 5 and 11, two QTLs for number of flowers per truss on chromosomes 2 and 5, and five QTLs for fruit weight on chromosomes 1, 2, 3, 9 and 12 are identified.

关键词： tomato ssr markers genetic mapping first flower node number of flowers per truss fruit weight.

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ssr markers for Fusarium Head Blight Resistance QTLs in Three Wheat Populations

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Agricultural Sciences in China 2003年第9期2卷 987-993页

作者： RENLi-juan SHENXiao-rong ZHOUMiao-ping ZHANGXu MAHong-xiang LUWei-zhong PaulNichoson InstiuteofGeneticsandPhysiology JiangsuAcademyofAgriculturalSciencesNanjing210014P.R.China DepartmentofAgronomy PurdueUniversityWestLafayette47907-1150USA DepartmentofDiseaseandStressBiology JohnInnesCentreNorwichNR47UHUK）

The objective of this research is to identify DNA markers linked to QTLs controlling FHB resistance in wheat, and to compare if the QTLs in three resistant germplasm are common. Three wheat recombinant inbred populations derived from the crosses between Alondra (susceptible) and three resistant lines, Wangshuibai, Sumai3, and 894037, respectively, were evaluated for reaction to Fusarium graminearum in greenhouse and in field conditions over years. Simple sequence repeat (ssr) markers were screened in the populations and regression analysis was used to identify markers associated with FHB resistance. For the population of Sumai3 (resistant)/Alondra (susceptible), which contained 161 recombinant inbred lines, two ssr markers located on chromosome 3B were found to be associated with resistant QTLs. These markers accounted for 2.66.7% phenotypic variation. The 894037 (resistant)/Alondra (susceptible) population was consisted of 147 recombinant inbred lines. A total of 59 ssr primers were screened in this population and seven of them were linked to resistant QTLs. The QTLs on chromosome 3B accounted for 47.4% phenotypic variation. Minor QTLs were also located on 2D, 7A, 6B, and 4B chromosomes, and the resistant QTLs on 2D and 4B chromosomes were from Alondra. The last population of 80 recombinant inbred lines was from the cross Wangshuibai (resistant)/Alondra (susceptible). A total of 120 ssr primers were screened in this population, eight of which were linked to resistant QTLs. These markers were located on 3B, 4B, 2D, 4D, and 6D (uncertain) chromosomes respectively. The QTLs on chromosome 3B accounted for 8.927.0% phenotypic variation. The resistant QTLs on chromosomes 4B and 6D (uncertain) were from Alondra. The other QTLs were from Wangshuibai. ssr markers linked to resistant QTLs on chromosome 3B were found in all three populations, and account for higher phenotypic variation. So these markers should be useful in marker assisted selection.

关键词： Wheat Resistance to FHB RILs ssr markers

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Development of polymorphic ssr markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma

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BIOCELL 2022年第11期46卷 2489-2495页

作者： XIAOJUN ZHOU XIAOYU LU XUBO WANG College of Life Science Luoyang Normal UniversityLuoyang471934China

Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific *** on the reduced-representation sequencing(RRS)technology of RAD-Seq,this study conducted high-throughput Illumina paired-end sequencing to find ssr marker information in the genome of ***,and to screen and verify polymorphism of ssr *** obtained 5.5G of high-quality data using *** total number of contigs of the RAD tags was 299,376,with the maximum contig length of 2,062 bp and the average length of 445 *** these sequences,we identified 20,718 ssr loci,with a distribution density of one ssr per 6.45 kb(1/6.45 kb).Among all ssrs,dinucleotides(52.00%)were the most detected ssrs,followed by mononucleotides(21.63%).AG/CT was the dominant motif in the ssr loci,accounting for 34.8%.Primers were successfully designed for 14,593 loci,and 100 pairs of these primers were randomly selected for chemical synthesis and validated by ssr-PCR amplification in 20 individuals of ***-nine primers were able to amplify the target *** 3.0 software was used to analyze the selected 20 ssr loci with good *** the 20 ssr markers,the number of alleles ranged from 4 to 9,and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to 0.875,*** information content of polymorphic loci ranged from 0.463 to 0.848,with an average value of *** them,there were 18 highly polymorphic loci,and 20 ssr loci did not deviate from the Hardy-Weinberg ***,the 20 pairs of ssr primers were used to conduct PCoA analysis based on Nei’s genetic distance of 51 individuals from three *** results showed that these ssr markers could distinguish genetic differences based on different geographical locations.

关键词： Cluster analysis E.pleiosperma RAD-Seq Rare species ssr markers

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Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with ssr markers

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Agricultural Sciences in China 2008年第9期7卷 1037-1045页

作者： LI Lu-jiang YANG Ke-cheng PAN Guang-tang RONG Ting-zhao Maize Research Institute Sichuan Agricultural University~Key Laboratory of Crop Genetic Resources and Improvement Ministry of Education Ya＇ an 625014 P.R.China

Two cycles of biparental mass selection （MS） and one cycle of half-sib-S3 family combining selection （HS-S3） for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously. The genetic diversity of 8 maize populations, including both the basic populations and their developed populations, were evaluated by 30 ssr primers. On the 30 ssr loci, a total of 184 alleles had been detected in these populations. At each locus, the number of alleles varied from 2 to 14, with an average of 6.13. The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations, respectively. There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity. The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations. Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations. The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations. The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations. All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations, and the genetic diversity was maintained during MS, whereas the genetic diversity of populations decreased after HS-S3. This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS, whereas the populations become more homozygotic after HS-S3.

关键词： maize recurrent selection genetic diversity ssr markers biparental mass selection (MS) half-sib-S3 familycombining selection (HS-S3)

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