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Analysis of SSRs Uncovers Hierarchical Structure and Genetic Diversity in Chinese Soybean Landraces

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Agricultural Sciences in China 2010年第12期9卷 1739-1748页

作者： li Ying-hui Marinus J M Smulders CHANG Ru-zhen qiu li-juan The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization Ministry of Agriculture (MOA)/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 P.R. China Plant Research International Wageningen UR Wageningen 6700 AA The Netherland

For clarifying the hierarchical patterns of population structure of soybean landraces in China, the seven clusters previously identified using Bayesian clustering of 1 504 soybean landraces based on SSR markers genotyping data were further analyzed. Using the largest value of AK, these landraces could be split into 20 sub-clusters, which was supported by highly significant pairwise Fst-values and generally in accordance with the geographic origin and sowing types. The autumn-sowing types ended up in one distinct sub-cluster from the otherwise summer-sowing type, where the autumn- sowing types are most likely derived from. The division into 20 sub-clusters explained 7.3% of the genetic variation, next to 9.7% present among the seven clusters, 81.1% residing among landraces within sub-clusters, and 1.9% within the landraces. The distribution pattern of genetic diversity among the sub-clusters of each cluster was uneven, with two HSuM sub-clusters （Central China） and some South China sub-clusters showing significantly higher level of genetic diversity.

关键词： soybean landrace hierarchical structure diversity

Development and identification of glyphosate-tolerant transgenic soybean via direct selection with glyphosate

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Journal of Integrative Agriculture 2020年第5期19卷 1186-1196页

作者： GUO Bing-fu HONG Hui-long HAN Jia-nan ZHANG li-juan liU Zhang-xiong GUO Yong qiu li-juan National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/MOA Key Lab of Soybean Biology/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081P.R.China Jiangxi Province Key Laboratory of Oilcrops Biology/Crops Research Institute Jiangxi Academy of Agricultural SciencesNanchang 330200P.R.China

Glyphosate-tolerant soybean is the most widely planted genetically modified crop worldwide. However, soybean remains recalcitrant to routine transformation because of the low infection efficiency of Agrobacterium to soybean and lack of useful selectable markers. In this study, several Agrobacterium strains and cell densities were compared by transient expression of the GUS gene. The results showed that Agrobacterium strain Ag10 at cell densities of OD_(600) of 0.6–0.9 yielded the highest infection efficiency in Agrobacterium-mediated soybean cotyledonary node transformation system. Meanwhile, a simple and rapid method was developed for identification of glyphosate tolerance in putative T_0 transgenic plants, consisting of spotting plantlets with 1 μL Roundup~?. The whole cycle of genetic transformation could be shortened to about 3 mon by highly efficient selection with glyphosate during the transformation process and application of the spot assay in putative T_0 transgenic plantlets. The transformation frequency ranged from 2.9 to 5.6%. This study provides an improved protocol for development and identification of glyphosate-tolerant transgenic soybeans.

关键词： soybean transformation spot assay glyphosate selection transgenic plants

The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans

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Journal of Integrative Agriculture 2016年第2期15卷 262-270页

作者： li Yan-fei HONG Hui-long li Ying-hui MA Yan-song CHANG Ru-zhen qiu li-juan National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Lab of Germplasm Utilization Ministry of Agriculture/Institute of Crop ScienceChinese Academy of Agricultural Sciences College of Agriculture Northeast Agricultural University Soybean Research Institute Heilongjiang Academy of Agricultural Sciences

The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ *** growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） and hence a larger R/V ***,the genetic basis of the domestication of soybean from wild materials is ***,a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants（PAVs） while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different *** major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine *** genotyping was largely consistent with the taxonomic status,although a few accessions were intermediate between the two major clades *** diversity was much higher in the wild germplasm than in the cultivated materials.A significant domestication signal was detected at 11 of the PAVs at 0.01 *** particular,this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean.A significant marker-trait association with R/V ratio was detected at 14 of the PAVs,but stripping out population structure reduced this to *** results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.

关键词： wild soybean cultivated soybean genomic structure variation interspecific differentiation photoperiod

Co-treatment with surfactant and sonication signifi cantly improves Agrobacterium-mediated resistant bud formation and transient expression efficiency in soybean

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Journal of Integrative Agriculture 2015年第7期14卷 1242-1250页

作者： GUO Bing-fu GUO Yong WANG Jun ZHANG li-juan JIN Long-guo HONG Hui-long CHANG Ru-zheng qiu li-juan College of Agriculture Northeast Agricultural University The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Institute of Crop Science Chinese Academy of Agricultural Sciences College of Agriculture Yangtze University

Soybean is a widely planted genetically modified crop around the world. However, it is still one of the most recalcitrant crops for genetic transformation due to the difficulty of regeneration via organogenesis and some factors that affect the transformation efficiency. The percentages of resistant bud formation and transient expression efficiency are important indexes reflecting the regeneration and transformation efficiency of soybean. In this study, the percentages of resistant bud formation and transient expression of 13-glucuronidase （GUS） were compared after treatment with sonication or surfactant and co-treatment with both. The results showed that treatment with either sonication or surfactant increased the percentage of resistant bud formation and transient expression efficiency. The highest percentages were acquired and significantly improved when cotyledon node explants were co-treated with sonication for 2 s and surfactant at 0.02% （v：v） using two different soybean genotypes, Jack and Zhonghuang 10. The improved transformation efficiency of this combination was also evaluated by development of herbicide-tolerant soybeans with transformation efficiency at 2.5-5.7% for different geno- types, which was significantly higher than traditional cotyledonary node method in this study. These results suggested that co-treatment with surfactant and sonication significantly improved the percentages of resistance bud formation, transient expression efficiency and stable transformation efficiency in soybean.

关键词： soybean genetic transformation sonication surfactant co-treatment

Development of Soybean EST-SSR Markers and Their Use to Assess Genetic Diversity in the Subgenus Soja

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Agricultural Sciences in China 2010年第10期9卷 1423-1429页

作者： liU Yu-lin li Ying-hui ZHOU Guo-an Uzokwe N CHANG Ru-zhen CHEN Shou-yi qiu li-juan The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm Utilization Ministry of Agricuhure/lnstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 P.R. China Plant Gene Research Centre National Key Laboratory of Plant Genomics/Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 P.R. China

Developing expressed sequence tag-derived SSR （EST-SSR） markers is imperative in genetic research. In this paper, we reported 37 EST-SSR markers which were developed from 286 unigenes obtained from soybean cDNA library. Among the 286 markers designed for the 4 accessions of Glycine max and 6 of its wild progenitor （G. soja） within the subgenus Soja, 209 markers amplified DNA fragments, taking 73.1% and 37 markers appeared to be polymorphic, which was 12.9% of the total. The 37 loci detected a total of 142 alleles, while the PIC values varied from 0.194 to 0.794. Both the number of alleles per locus and PIC value were significantly related to the SSR motif. Six EST-SSR loci may be fixed for different alleles between G. max and G. soja since they were particularly polymorphic among the 6 G. soja accessions. A neighbor-joining tree placed the G. max accessions together as a group within the G. soja, though the average genetic distance among G. soja accessions was much higher. These new EST-SSRs markers will be useful for genetic diversity analysis, genetic mapping construction and gene discovery in Soja subgenus.

关键词： EST-SSR diversity Soja subgenus

Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean(Glycine max ***.)

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Journal of Integrative Agriculture 2022年第7期21卷 1903-1912页

作者： liU Chen TIAN Yu liU Zhang-xiong GU Yong-zhe ZHANG Bo li Ying-hui NA Jie qiu li-juan School of life Sciences Liaoning Normal UniversityDalian 116081P.R.China National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization Ministry of Agriculture and Rural Affairs/Institute of Crop SciencesChinese Academy of Agricultural ScienceBeijing 100081P.R.China School of Plant and Environmental Sciences Virginia Polytechnic Institute and State UniversityBlacksburgVA 24060USA

With the development of sequencing technology, insertions-deletions(InDels) have been increasingly reported to be involved in the genetic determination of agronomical traits. However, most studies have focused on the identification and application of short-InDels(1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels(>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373(ZP) and Zhonghuang 13(ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704(19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL(qP H16) underlying plant height was further analyzed, and it was found that 26 out of 35(74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

关键词： soybean plant height whole genome re-sequencing long-InDels QTL

Identification of the genetic locus associated with the crinkled leaf phenotype in a soybean(Glycine max L.)mutant by BSA-Seq technology

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Journal of Integrative Agriculture 2022年第12期21卷 3524-3539页

作者： Kingsley OCHAR SU Bo-hong ZHOU Ming-ming liU Zhang-xiong GAO Hua-wei Sobhi FLAMLOM qiu li-juan National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081P.R.China College of Agriculture Northeast Agricultural University/Key Laboratory of Soybean BiologyMinistry of EducationHarbin 150030P.R.China School of Agriculture Yangtze UniversityJingzhou 434025P.R.China Plant Production Department Faculty of Agriculture Saba BashaAlexandria UniversityAlexandria 21531Egypt

The leaf is the main photosynthetic organ of plants,and it plays a significant role in the yield of crop *** the causal mutations and candidate genes that underlie leaf phenotypic variation is an important breeding target in soybean grain yield *** ethyl methyl sulfonate(EMS)-induced soybean mutant DWARFCRINKLEDLEAF1(DCL1)with an aberrant crinkled leaf phenotype was identified in the background of the soybean cultivar Zhongpin 661(Zp661).We constructed an F2 segregating population from a cross between Zp661 and DCL1 in order to investigate the genomic locus associated with the crinkled leaf *** bulk segregant analysis(BSA)combined with the whole-genome resequencing method,the Euclidean distance(ED)correlation algorithm detected 12 candidate genomic regions with a total length of 20.32 Mb that were linked to the target *** a comparative analysis of the sequence data for the wild-type and mutant pools,only one single nucleotide mutation(C:G>T:A)located on the first exon of Glyma.19G207100 was found to be associated with the *** gene validation based on a CAPS marker derived from the detected single-nucleotide polymorphism(SNP)indicated a nucleotide polymorphism between the two ***,our findings reveal that Glyma.19G207100,which is renamed as GLYCINE MAX DWARF CRINKLED LEAF 1(GmDCL1),is a promising candidate gene involved in the morphogenesis of the crinkled leaf trait of the soybean mutant *** study provides a basis for the functional validation of this gene,with prospects for soybean breeding targeting grain yield enhancement.

关键词： soybean mutant crinkled leaf BSA GmDCL1

QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean

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Journal of Integrative Agriculture 2022年第4期21卷 933-946页

作者： TIAN Yu YANG Lei LU Hong-feng ZHANG Bo li Yan-fei liU Chen GE Tian-li liU Yu-lin HAN Jia-nan li Ying-hui qiu li-juan National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization Ministry of Agriculture and Rural Affairs/Institute of Crop SciencesChinese Academy of Agricultural ScienceBeijing 100081P.R.China Novogene Bioinformatics Institute Beijing 100015P.R.China School of Plant and Environmental Sciences Virginia Polytechnic Institute and State UniversityBlacksburgVA 24060USA School of life Sciences Liaoning Normal UniversityDalian 116081P.R.China College of Forestry Northwest A&F UniversityYangling 712100P.R.China

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.

关键词： soybean plant height whole genome re-sequencing bin map QTL

Establishment and application of an accurate identification method for fragrant soybeans

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Journal of Integrative Agriculture 2021年第5期20卷 1193-1203页

作者： ZHANG Yong-fang ZHANG Chun-yan ZHANG Bo YIN Man HONG Hui-long YU li-li GAO Hua-wei GU Yong-zhe liU Zhang-xiong li Fu-heng qiu li-juan College of life Sciences Northeast Agricultural UniversityHarbin 150030P.R.China College of life Sciences Shanxi Datong UniversityDatong 037009P.R.China National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Germplamsm Utilization Ministry of Agriculture and Rural Affairs/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081P.R.China School of Plant and Environmental Sciences Virginia Polytechnic Institute and State UniversityBlacksburgVA 24060USA

In order to screen the aroma characteristics of soybean,a new method was established which can quickly quantify the content of 2-acetyl-1pyrroline(2-AP),an important compound related to soybean aroma,using gas chromatography-mass spectrometry(GC-MS).Based on peak profile,total peak area and retention time as test indexes,an accurate identification method for fragrant soybeans was *** optimum parameters of the protocol consisted of column temperature70℃,sample injector temperature 180℃,optimum extraction alcohol content 1 m L,Na Cl content 0.1 g,ultrasonication time10 min,and extraction time 1 h,which were established by using the orthogonal test of single factors and three factors with four levels(L_9(3)^4).2-AP content of leaves had significant correlations with seeds,which were easier to *** protocol was simple and easy to carry out,consumed only small amounts of reagents,and provided accurate and reliable results with good reproducibility.A total of 101 soybean genotypes from different geographical sources were analyzed using this *** results showed that the average content of 2-AP was 0.29 mg L^(–1),ranging from 0.094 to 1.816 mg L^(–1),and the genetic diversity index was *** all genotypes-tested,they were classified into three grades,including seven elite genotypes identified as"grade one fragrant soybeans",which were Zhonglong 608,Heinong 88,Ha13-2958,Hongmiandou,Heinong 82,Huangmaodou,and Jiyu *** results provide both an identification technique and several elite aroma genotypes for gene discovery and good quality breeding in soybean.

关键词： soybean 2-acetyl-1pyrroline GC-MS quantification method germplasm