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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

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

AKINβ1 is Involved in the Regulation of Nitrogen Metabolism and Sugar Signaling in Arabidopsis

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Journal of Integrative Plant Biology 2009年第5期51卷 513-520页

作者： Xiao-Fang li Yu-Ju li ying-hui An li-Jun Xiong Xing-Hua Shao Yang Wang Yue Sun School of life Sciences East China Normal University Shanghai 200062 China

Sucrose non-fermenting-l-related protein kinase 1 （SnRK1） has been located at the heart of the control of metabolism and development in plants. The active SnRK1 form is usually a heterotrimeric complex. Subcellular localization and specific target of the SnRK1 kinase are regulated by specific beta subunits. In Arabidopsis, there are at least seven genes encoding beta subunits, of which the regulatory functions are not yet clear. Here, we tried to study the function of one beta subunit, AKINβ1. It showed that AKINβ1 expression was dramatically induced by ammonia nitrate but not potassium nitrate, and the investigation of AKINβ1 transgenic Arabidopsis and T-DNA insertion lines showed that AKINβ1 negatively regulated the activity of nitrate ruductase and was positively involved in sugar repression in early seedling development. Meanwhile AKIN/β1 expression was reduced upon sugar treatment （including mannitol） and did not affect the activity of sucrose phosphate synthase. The results indicate that AKIN/β1 is involved in the regulation of nitrogen metabolism and sugar signaling.

关键词： AKIN/β1 metabolism nitrate reductase sucrose phosphate synthase sugar signaling

Accuracy of a combined score of zygote and embryo morphology for selecting the best embryos for IVF

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2008年第8期9卷 649-655页

作者： Yu-li QIAN ying-hui YE Chen-ming XU Fan JIN He-feng HUANG Department of Reproductive Endocrinology Women＇s Hospital School of Medicine Zhejiang University Hangzhou 310006 China

Objective:To evaluate the accuracy of a scoring system combining zygote and embryo morphology in predicting the outcome of in vitro fertilization (IVF) treatment. Methods: In a study group, 117 consecutive IVF or intracytoplasmic sperm injection (ICSI) cycles with embryo transfer were carried out and 312 embryos were scored using a combined scoring system (CSS) of zygote and embryo morphology before transplantation. In a control group, a total of 420 IVF or ICSI cycles were carried out and 1176 embryos were scored using a cumulative embryo score (CES). The effects of the combined scoring system on the embryo implantation rate and pregnancy rate per cycle were analyzed. Results: Using the combined scoring system, the embryo implan-tation rate (27.6%) and the clinical pregnancy rate (48.7%) were significantly higher than those in the control group (20.8% and 38.6%, respectively). Also, the implantation rate of embryos scoring ≥70 (38.5%: 82 sacs/213 embryos) was significantly higher (P<0.001) than that of embryos scoring <70 (4%: 4 sacs/99 embryos). The pregnancy rate of patients with embryos scoring ≥70 using the combined scoring system (66.7%) was significantly higher (P<0.001) than that of patients with embryos scoring ≥20 using the cumulative embryo score (59.0%). Conclusion: The results suggest that selecting embryos with a high score (≥70) using the combined scoring system could increase the implantation rate and pregnancy rate, and that using a scoring system combining assessments of human zygotes and pre-implantation embryos might predict IVF outcomes more accurately than using a cumula-tive embryo score.

关键词： Embryo score Combined scoring system (CSS) Implantation In vitro fertilization (IVF) Pregnancy

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

Mechanism of Sterility and Breeding Strategies for Photoperiod/Thermo-Sensitive Genic Male Sterile Rice

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Rice science 2010年第3期17卷 161-167页

作者： CHEN li—yun XIAO ying-hui LEI Dong-yang Rice Research Institute Hunan Agricultural University Changsha 410128 China

To understand the male sterility mechanism of photoperiod/thermo-sensitive genic male sterile [P（T）GMS] lines in rice, the research progress on genetics of photoperiod and/or temperature sensitive genic male sterility in rice was reviewed. A new idea was proposed to explain the sterility mechanism of P（T）GMS rice. The fertility transition from sterile to fertile is the result of cooperative regulation of major-effect sterile genes with photoperiod and/or temperature sensitive genes, but not the so-called pgms gene in P（T）GMS rice. The minor-effect genes, which exhibit accumulative effect on sterility, are the important factors for the critical temperature of sterility transition. The more minor-effect genes the sterile line holds, the lower the critical temperature of sterility transition is. The critical temperature of sterility transition will be invariable if all the minor-effect genes are homozygous. The strategies for breeding P（T）GMS rice were also proposed. The selective indices of critical photoperiod and temperature for sterility transition should be set according to varietal type and ecological region. Imposing selection pressure is a key technology for breeding P（T）GMS rice with lower critical temperature for sterility, and improving the comprehensive performance of the whole traits and combining ability is vital for breeding P（T）GMS rice lines.

关键词： rice photoperiod/thermo-sensitive genic male sterility mechanism of sterility breeding strategy

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

Three Important Transcription Factors Related to lipogenesis and Adipogenesis in Mammal

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Journal of Northeast Agricultural University(English Edition) 2010年第3期17卷 62-75页

作者： ZHANG ying li hui College of Animal Sciences and Technology Northeast Agricultural University Harbin 150030 China

lipid metabolism and adipocyte differentiation are reglulated by networking of transcription factors. It is generally known that three factors, peroxisome proliferator-activated receptor y （PPARγ）, CCAAT/element-binding protein a （C/EBPa） and sterol regulatory element binding protein-1 （SREBP1）, play fundamental roles in metabolic pathways. And they are also important in adipocyte differentiation. Expressions of these factors are regulated by some compounds such as fatty acids or some steroid hormones （insulin） which is stimulated by the nutritional level. Furthermore, these factors are related to some metabolic diseases including type II diabetes and obesity, Lots of researches have focused on relationships between the factors and the genetic diseases. Different functions of factors on inducing the adipocyte differentiation are other hot spots according to previous studies. This paper summarized these studies and gave a limpid description of structures and functions of these genes.

关键词： PPARγ C/EBPa SREBP1 lipogenesis adipogenesis