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SPP-extractor:Automatic phenotype extraction for densely grown soybean plants

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作物学报:英文版 2023年第5期11卷 1569-1578页

作者： Wan Zhou Yijie Chen Weihao Li Cong Zhang Yajun Xiong Wei Zhan Lan Huang Jun Wang lijuan qiu College of Computer Science Yangtze UniversityJingzhou 434023HubeiChina College of Agriculture Yangtze UniversityJingzhou 434025HubeiChina national key facility for gene resources and genetic improvement/Institute of crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China MARA key Laboratory of Sustainable crop Production in the Middle Reaches of the Yangtze River(Co-construction by Ministry and Province) College of AgricultureYangtze UniversityJingzhou 434025HubeiChina

Automatic collecting of phenotypic information from plants has become a trend in breeding and smart *** mature soybean plants at the harvesting stage,which are dense and overlapping,we have proposed the SPP-extractor(soybean plant phenotype extractor)algorithm to acquire phenotypic ***,to address the mutual occultation of pods,we augmented the standard YOLOv5s model for target detection with an additional attention *** resulting model could accurately identify pods and stems and could count the entire pod set of a plant in a single ***,considering that mature branches are usually bent and covered with pods,we designed a branch recognition and measurement module combining image processing,target detection,semantic segmentation,and heuristic *** results on real plants showed that SPP-extractor achieved respective R^(2) scores of 0.93–0.99 for four phenotypic traits,based on regression on manual measurements.

关键词： Soybean phenotype Branch length Computer vision A*algorithm Phenotype acquisition

Gm Ms1 encodes a kinesin-like protein essential for male fertility in soybean(Glycine max L.)

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Journal of Integrative Plant Biology 2021年第6期63卷 1054-1064页

作者： Muhammad Nadeem Andong Chen Huilong Hong Dongdong Li Jiajia Li Duo Zhao Wei Wang Xiaobo Wang lijuan qiu School of Agronomy Anhui Agricultural UniversityHefei 230036China The national key facility for crop gene resources and genetic improvement(NFCRI)/key Laboratory of crop gene Resource and Germplasm Enhancement(MOA) Institute of Crop SciencesThe Chinese Academy of Agricultural SciencesBeijing 100081China

The application of heterosis is a promising approach for greatly increasing yield in soybean(Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we report the cloning of the gene underlying the soybean male-sterile mutant ms-1,which has been widely used for recurrent selection in soybean breeding programs. We initially delimited the ms1 locus to a 16.15 kb region on chromosome13, based on SLAF_BSA sequencing followed by genotyping of an F_(2) population segregating for the locus. Compared with the same region in fertile plants, the mutant region lacks a sequence of approximately 38.7 kb containing five protein-coding genes, including an ortholog of the kinesin-like protein gene NACK2, named Gm Ms1. The Gm Ms1 knockout plants generated via CRISPR/Casmediated gene editing displayed a complete malesterile phenotype. Metabolic profiling showed that fertile anthers accumulated starch and sucrose normally, whereas sterile anthers had higher anthocyanin levels and lower flavonoid levels and lower antioxidant enzyme activities. These results provide insights into the molecular mechanisms governing male sterility and demonstrate that Gm Ms1 could be used to create male-sterile lines through targeted mutagenesis. These findings pave the way for designing seed production technology and an intelligent male-sterile line system to utilize heterosis in soybean.

关键词： metabolome sequencing nuclear male sterility soybean third generation sequencing transcriptome sequencing

Identification and Functional Analysis on Abiotic Stress Response of Soybean Cl^- Channel gene GmCLCnt

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Agricultural Sciences in china 2010年第2期9卷 199-206页

作者： ZHOU guo-an qiu Li-juan The national key facility for crop gene resources and genetic improvement （NFCRI）/key Lab of Germplasm Utilization Ministry of Agriculture/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 P.R.China

The Cl^- homeostasis was known as the major mechanism of soybean to achieve NaCl tolerance, but studies on the role of chloride channel under abiotic stress were relatively few. We cloned a putative CLC-type chloride channel gene GmCLCnt from soybean via RACE and it was predicted to encode a protein of 783 amino acids with 9 possible transmembrane domains and 2 tandem CBS domains. Real-time RT-PCR analysis showed that the GmCLCnt gene was expressed in all tissues of soybean but enriched in leaves and its expression was induced by NaCl, polyethylene glycol （PEG）, coldness and ABA treatments. The Arabidopsis seedlings overexpressing GmCLCnt were more tolerant to higher concentration of NaCl than those of wild type. The results suggested that the GmCLCnt may be a CLC-type chloride channel and play an important role in salt tolerance.

关键词： GmCLCnt gene chloride channel salt tolerance soybean

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

Identification of genes for drought resistance and prediction of gene candidates in soybean seedlings based on linkage and association mapping

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The crop Journal 2022年第3期10卷 830-839页

作者： Yanjun Zhang Zhangxiong Liu Xingrong Wang Yue Li Yongsheng Li Zuowang Gou Xingzhen Zhao Huilong Hong Honglei Ren Xusheng Qi lijuan qiu Institute of crop Gansu Academy of Agricultural SciencesLanzhou 730070GansuChina national key facility for gene resources and genetic improvement/key Laboratory of crop Germplasm Utilization Ministry of Agriculture/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Maize Research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086HeilongjiangChina

Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of *** extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of soybean growth:the number and vigor of seedlings will affect growth and yield at ***,it is important to study the drought resistance of soybean *** this study,a recombinant inbred line(RIL)population comprising 234 F_(6:10)lines(derived from Zhonghuang35×Jindou 21)and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these *** a genetic map constructed by single nucleotide polymorphism(SNPs)markers,18 quantitative trait loci(QTL)on 7 soybean chromosomes were identified in two *** included 9 QTL clusters identified in the RIL ***-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis(GWAS)in the panel of accessions,including 69 significant SNPs(-log_(10)(P)≥3.97).A combination of the two populations revealed that two SNPs(-log_(10)(P)≥3.0)fell within two of the QTL(qPH7-4 and qPH7-6)confidence *** not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents,involving Glyma.07 g093000,Glyma.07 g093200,Glyma.07 g094100 and Glyma.07 *** previously unreported new gene related to drought stress,Glyma.07 g094200,was found by regional association *** significant SNP CHR7-17619(G/T)was within an exon of the Glyma.07 g094200 *** the RIL population,the DSP value of the"T"allele of CHR7-17619 was significantly(Pgenes in soybeans at the seedling stage.

关键词： Candidate genes Drought tolerance Glycine max QTL SNP

Geographical distribution of GmTfl1 alleles in Chinese soybean varieties

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The crop Journal 2015年第5期3卷 371-378页

作者： Guifeng Liu Lin Zhao Benjamin J.Averitt Ying Liu Bo Zhang Ruzhen Chang Yansong Ma Xiaoyan Luan Rongxia Guan lijuan qiu Soybean Research Institute Northeast Agricultural University Department of crop and Soil Environmental Sciences VA Polytechnic Institute and State University The national key facility for crop gene resources and genetic improvement (NFCRI) Institute of Crop ScienceChinese Academy of Agricultural Sciences Heilongjiang Academy of Agricultural Sciences

Stem growth habit is an important agronomic trait in soybean and is subject to artificial selection. This study aimed to provide a theory for genotypic selection of stem growth habit for breeding purposes by analyzing the alleles of Gm Tfl1 gene in Chinese soybean varieties and establishing a database of Gm Tfl1 variation. Using knowledge of insertion and deletion(Indel) in the non-coding region and four single-nucleotide polymorphisms(SNPs) in the coding sequences of the Gm Tfl1 gene, four CAPS and one Indel markers were developed and used to test 1120 Chinese soybean varieties. We found that the dominant Gm Tfl1 allele was prevalent in accessions from the Northern ecoregion, whereas the recessive allele, Gmtfl1, was more common in the Southern ecoregion, and the proportions of Gm Tfl1 and recessive alleles were respectively 40.1% and 59.9% in the Huang-Huai ecoregion. The proportion of Gm Tfl1 decreased and that of Gmtfl1 increased, gradually from north to south. Allele Gm Tfl1-a was present in higher proportions in the Huang-Huai spring, Huang-Huai summer, and Northern spring sub-ecoregions than that in the other sub-ecoregions. Gm Tfl1-b was common in the Northeast spring, Northern spring and Southern summer sub-ecoregions. Gmtfl1-ta was found mainly in the Huang-Huai spring,Huang-Huai summer and Southern spring sub-ecoregions. The Gmtfl1-ab allele was distributed in all six soybean sub-ecoregions. The Gmtfl1-bb allele was distributed mainly in the Huang-Huai spring and summer and Southern spring and summer sub-ecoregions,but the Gmtfl1-tb allele was detected only in the Huang-Huai summer sub-ecoregion. The distributions of Gm Tfl1 and Gmtfl1 have shown no large changes in nearly 60 years of breeding, but the frequency of the recessive genotype Gmtfl1 has shown a rising trend in the last 20 years. This study provides a theoretical foundation for breeding new soybean varieties for different ecoregions.

关键词： Soybean Stem growth habit Gm Tfl1 Distribution

Identification of a novel seed size associated locus SW9-1 in soybean

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The crop Journal 2019年第4期7卷 548-559页

作者： Jiajia Li Jinghui Zhao Yinghui Li Yali Gao Sunan Hua Muhammad Nadeem Genlou Sun Wenming Zhang Jinfeng Hou Xiaobo Wang lijuan qiu School of Agronomy Anhui Agricultural University Hefei 230036 Anhui China The national key facility for crop gene resources and genetic improvement (NFCRI)/key Laboratory of crop gene Resource and Germplasm Enhancement (MOA) Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China Biology Department Saint Mary's University Halifax NS B3H 3C3 Canada College of Horticulture Anhui Agricultural University Hefei 230036 Anhui China

Seed size is one of the vital traits determining seed appearance, quality, and yield. Untangling the genetic mechanisms regulating soybean 100-seed weight (100-SW), seed length and seed width across environments may provide a theoretical basis for improving seed yield. However, there are few reports related to QTL mapping of 100-SW across multiple ecological regions. In this study, 21 loci associated with seed size traits were identified using a genome-wide association of 5361 single nucleotide polymorphisms (SNPs) across three ecoregions in china, which could explain 8.12%–14.25% of the phenotypic variance respectively. A new locus, named as SW9-1 on chromosome 9 that explained 10.05%–10.93% of the seed weight variance was found significantly related to seed size traits, and was not previously reported. The selection effect analysis showed that SW9-1 locus has a relatively high phenotypic effect (13.67) on 100-SW, with a greater contribution by the accessions with bigger seeds (3.69) than the accessions with small seeds (1.66). Increases in seed weight were accompanied by increases in the frequency of SW9-1T allele, with >90% of the bred varieties with a 100-SW >30 g carrying SW9-1T. Analysis of SW9-1 allelic variation in additional soybean accessions showed that SW9-1T allele accounting for 13.83% of the wild accessions, while in 46.55% and 51.57% of the landraces and bred accessions, respectively, this results indicating that the SW9-1 locus has been subjected to artificial selection during the early stages of soybean breeding, especially the utilization of SW9-1T in edamame for big seed. These results suggest that SW9-1 is a novel and reliable locus associated with seed size traits, and might have an important implication for increasing soybean seed weight in molecular design breeding. Cloning this locus in future may provide new insights into the genetic mechanisms underlying soybean seed size traits.

关键词： Soybean [Glycine max (L.) Merr.] Seed size/weight SW9-1 Molecular breeding

genetic contribution of foreign germplasm to elite Chinese soybean (Glycine max) cultivars revealed by SSR markers

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Chinese Science Bulletin 2006年第9期51卷 1078-1084页

作者： QIN Jun CHEN Weiyuan GUAN Rongxia JIANG Chengxi LI Yinghui FU Yashu LIU Zhangxiong ZHANG Mengchen CHANG Ruzhen qiu lijuan national key facility of crop gene resources and genetic improvement Key Lab of Crop Gerrnplasm Resources & Biotechology (MOA) Institute of Crop Science Chinese Agricultural Academy of Sciences Beijing 100081 China Hebei Academy of Agricultural and Forestry Science Shijiazhuang 050031 China Heilongjiang Academy of Agricultural Science Suihua 152052 China

Simple sequence repeats (SSR) marker analysis, combined with pedigree analysis, was car- ried out to trace the genetic constitutes of Suinong 14 and Hefeng 25 in assessing the contribution of for- eign germplasm to those elite cultivars. The overall goal is to accumulate information for further effective utilization of foreign germplasm in Chinese soybean breeding programs. SSR clustering results indicated that the genetic base of elite Chinese soybean culti- vars, including Suinong 14 and Hefeng 25, were broadened and enhanced via introduction of Amsoy from the U.S. and Shishengchangye from Japan. The pedigree analysis showed a very high coefficient of parentage between Shishengchangye and Hefeng 25, between Shishengchangye and Suinong 14, and between Amsoy and Suinong 14. The genetic simi- larity between Suinong 14 and Hefeng 25 was 60.58%. Among 20 linkage groups, more genomic regions were transferred from Hefeng 25 to Suinong 14 in linkage group (LG) I, L and C2 than other LGs. Among the unique alleles of foreign parents, five specific loci in Amsoy were transferred to Suinong 14, and three loci from Shishengchangye to Suinong 14. Some SSR loci were proved to be correlated with phenotypes: two loci for seed size introgressed from Shishengchangye to Suinong 14, and one locus forprotein content from Amsoy to Suinong 14. These results indicate that the two foreign parents might have important contributions in the development of Suinong 14 and Hefeng 25.

关键词：大豆谱系分析 SSR 序列分析种质资源

genetic analysis and gene mapping of a dwarf and liguleless mutation in barley

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The crop Journal 2022年第4期10卷 1094-1102页

作者： Baojian guo Jiang Qi Dongfang Li Hongwei Sun Chao Lyu Feifei Wang Juan Zhu Ganggang guo Rugen Xu Jiangsu key Laboratory of crop Genomics and Molecular Breeding/key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu key Laboratory of crop genetics and Physiology Jiangsu Co-Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou 225009JiangsuChina Joint International Research Laboratory of Agriculture and Agri-Product Safety The Ministry of Education of ChinaYangzhou UniversityYangzhou 225009JiangsuChina key Laboratory of crop Germplasm resources and Utilization(MOA) The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Leaf development underlies crop growth and productivity and has been a major target of crop domestication and ***,most genes controlling leaf development in barley remain *** identified a dwarf and liguleless(dl)mutant derived by ethylmethane sulfonate *** dl mutant showed dramatic changes in shoot architecture compared with wild-type(Yangnongpi 5)*** lacking ligules,the dl mutant showed much shorter plant height(28 cm)than Yangnongpi 5(78 cm).By map-based cloning,the dl gene was localized to a 56.58-kb genomic interval on the long arm of chromosome 7.A C-to-T single-nucleotide substitution was identified at exon position 790,and is a functional mutation resulting in a proline-to-serine substitution at the 264th amino acid residue of ***,HORVU7Hr1G106960 was identified as the DL gene,encoding 269 amino acids and containing the Arabidopsis LSH1 and Oryza G1(ALOG)*** is highly similar to rice OsG1-LIKE 1/2(OsG1L1/2)and sorghum AWN1/AWN1-10 at the amino acid *** the dl mutant allele showed no expression changes in selected tissues by real-time PCR,we propose HORVU7Hr1G106960 as a candidate gene conferring the dwarf and liguleless phenotype in barley.

关键词： Barley EMS Liguleless ALOG Shoot architecture