National Center for Soybean Improvement

Nanjing, China

National Center for Soybean Improvement

Nanjing, China
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Li S.,Nanjing Agricultural University | Cao Y.,Nanjing Agricultural University | He J.,Nanjing Agricultural University | Zhao T.,Nanjing Agricultural University | And 5 more authors.
Theoretical and Applied Genetics | Year: 2017

Key message: The RTM-GWAS was chosen among five procedures to identify DTF QTL-allele constitution in a soybean NAM population; 139 QTLs with 496 alleles accounting for 81.7% of phenotypic variance were detected.Abstract: Flowering date (days to flowering, DTF) is an ecological trait in soybean, closely related to its ability to adapt to areas. A nested association mapping (NAM) population consisting of four RIL populations (LM, ZM, MT and MW with M8206 as their common parent) was established and tested for their DTF under five environments. Using restriction-site-associated DNA sequencing the population was genotyped with SNP markers. The restricted two-stage multi-locus (RTM) genome-wide association study (GWAS) (RTM-GWAS) with SNP linkage disequilibrium block (SNPLDB) as multi-allele genomic markers performed the best among the five mapping procedures with software publicly available. It identified the greatest number of quantitative trait loci (QTLs) (139) and alleles (496) on 20 chromosomes covering almost all of the QTLs detected by four other mapping procedures. The RTM-GWAS provided the detected QTLs with highest genetic contribution but without overflowing and missing heritability problems (81.7% genetic contribution vs. heritability of 97.6%), while SNPLDB markers matched the NAM population property of multiple alleles per locus. The 139 QTLs with 496 alleles were organized into a QTL-allele matrix, showing the corresponding DTF genetic architecture of the five parents and the NAM population. All lines and parents comprised both positive and negative alleles, implying a great potential of recombination for early and late DTF improvement. From the detected QTL-allele system, 126 candidate genes were annotated and χ2 tested as a DTF candidate gene system involving nine biological processes, indicating the trait a complex, involving several biological processes rather than only a handful of major genes. © 2017 Springer-Verlag GmbH Germany


He J.,Nanjing Agricultural University | Meng S.,Nanjing Agricultural University | Zhao T.,National Center for Soybean Improvement | Zhao T.,Nanjing Agricultural University | And 14 more authors.
Theoretical and Applied Genetics | Year: 2017

Key message: The innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding.Abstract: The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Our proposed GWAS procedure is characterized as a novel restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS, https://github.com/njau-sri/rtm-gwas). The Chinese soybean germplasm population (CSGP) composed of 1024 accessions with 36,952 SNPLDBs (generated from 145,558 SNPs, with reduced linkage disequilibrium decay distance) was used to demonstrate the power and efficiency of RTM-GWAS. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. A relatively thorough detection of QTL with their multiple alleles was achieved by RTM-GWAS compared with the linear mixed model method on 100-seed weight in CSGP. A QTL-allele matrix (402 alleles of 139 QTL × 1024 accessions) was established as a compact form of the population genetic constitution. The 100-seed weight QTL-allele matrix was used for genetic characterization, candidate gene prediction, and genomic selection for optimal crosses in the germplasm population. © 2017 Springer-Verlag GmbH Germany


Jiang H.,Nanjing Agricultural University | Jiang H.,National Center for Soybean Improvement | Jiang H.,Key Laboratory of Biology and Genetic Improvement of Soybean General | Li K.,Nanjing Agricultural University | And 6 more authors.
Archives of Virology | Year: 2017

We discovered a soybean mosaic virus (SMV) variant (4278-1) that caused systemic infections in Nicotiana benthamiana plants, resulting in stem stunting and leaf shriveling. The virus had a particle morphology and incubation period similar to those of other SMV isolates but differed from them in the leaf symptoms it caused when infecting soybean and N. benthamiana. The genome of this variant consisted of a 9994-nt single-stranded RNA, which was different from most of the other known SMV isolates (approximately 9600 nt). Interestingly, we found evidence that two recombination events (nt 1-476 and nt 1145-1349) had occurred between 4278-1 and a watermelon mosaic virus analogue (WMV analogue), in the 5’ untranslated region and the P1 cistron. © 2016, Springer-Verlag Wien.


Huang Z.,Henan Institute of Science and Technology | Tong C.,Nanjing Forestry University | Bo W.,Beijing Forestry University | Pang X.,Beijing Forestry University | And 5 more authors.
Briefings in Bioinformatics | Year: 2014

Despite a tremendous effort to map quantitative trait loci (QTLs) responsible for agriculturally and biologically important traits in plants, our understanding of how a QTL governs the developmental process of plant seeds remains elusive. In this article, we address this issue by describing a model for functional mapping of seed development through the incorporation of the relationship between vegetative and reproductive growth. The time difference of reproductive from vegetative growth is described by Reeve and Huxley's allometric equation. Thus, the implementation of this equation into the framework of functional mapping allows dynamic QTLs for seed development to be identified more precisely. By estimating and testing mathematical parameters that define Reeve and Huxley's allometric equations of seed growth, the dynamic pattern of the genetic effects of the QTLs identified can be analyzed. We used the model to analyze a soybean data, leading to the detection of QTLs that control the growth of seed dry weight. Three dynamic QTLs, located in two different linkage groups, were detected to affect growth curves of seed dry weight. The QTLs detected may be used to improve seed yield with marker-assisted selection by altering the pattern of seed development in a hope to achieve a maximum size of seeds at a harvest time. © The Author 2013. Published by Oxford University Press.


Bo W.,Beijing Forestry University | Fu G.,Utah State University | Wang Z.,Pennsylvania State University | Xu F.,Beijing Forestry University | And 8 more authors.
Briefings in Bioinformatics | Year: 2014

The recent availability of high-throughput genetic and genomic data allows the genetic architecture of complex traits to be systematically mapped. The application of these genetic results to design and breed new crop types can be made possible through systems mapping. Systems mapping is a computational model that dissects a complex phenotype into its underlying components, coordinates different components in terms of biological laws through mathematical equations and maps specific genes that mediate each component and its connection with other components. Here, we present a new direction of systems mapping by integrating this tool with carbon economy. With an optimal spatial distribution of carbon fluxes between sources and sinks, plants tend to maximize whole-plant growth and competitive ability under limited availability of resources. We argue that such an economical strategy for plant growth and development, once integrated with systems mapping, will not only provide mechanistic insights into plant biology, but also help to spark a renaissance of interest in ideotype breeding in crops and trees. © The Author 2013. Published by Oxford University Press.


Yang C.,Nanjing Agricultural University | Yang C.,National Center for Soybean Improvement | Yang C.,National Key Laboratory of Crop Genetics and Germplasm Enhancement | Zhao T.,Nanjing Agricultural University | And 8 more authors.
Plant Molecular Biology Reporter | Year: 2011

It is well accepted that somatic embryogenesis serves a primary role in plant regeneration. However, it is also a model system to explore the regulatory and morphogenetic events in the life of a plant. To date, a suite of genes that serve important roles in somatic embryogenesis have been isolated and identified. In the present study, a novel gene designated as GmSERK1 was isolated from soybean (Glycine max (L.) Merr). Sequence and structural analysis determined that the GmSERK1 protein, which encodes 624 amino acids, belongs to the somatic embryogenesis receptor-like kinase (SERK) gene family. GmSERK1 shared all the characteristic domains of the SERK family, including five leucine-rich repeats, one proline-rich region motif, transmembrane domain, and kinase domains. DNA gel blot analysis indicated that a single copy of the GmSERK1 gene resides in the soybean genome. The GmSERK1 tissue-specific and induced expression patterns were explored using quantitative real-time PCR. Dissimilar expression levels in various tissues under different treatments were found. In addition, transient expression experiments in onion epidermal cells indicated that the GmSERK1 protein was located on the plasma membrane. The results from this study suggested that GmSERK1, a member of the SERK gene family, exhibits a broader role in various aspects of plant development and function, in addition to its basic functions in somatic embryogenesis. © 2010 Springer-Verlag.


Chang S.,National Center for Soybean Improvement | Chang S.,Key Laboratory of Biology and Genetic Improvement of Soybean | Chang S.,Nanjing Agricultural University | Wang Y.,Nanjing Agricultural University | And 13 more authors.
PLoS ONE | Year: 2013

Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean. © 2013 Chang et al.


Korir P.C.,Nanjing Agricultural University | Korir P.C.,National Center for Soybean Improvement | Korir P.C.,National Key Laboratory for Crop Genetics and Germplasm Enhancement | Zhao T.,Nanjing Agricultural University | And 5 more authors.
Frontiers of Agriculture in China | Year: 2010

To determine an appropriate indicator and a suitable stage for evaluating tolerance of soybeans to aluminum (Al) toxin is one of the keys to effective breeding for the trait. Seventeen accessions selected as tolerant from a previous test program by using average membership index (FAi) as indicator, plus one tolerant (PI.416937) and one sensitive (NN1138-2) check, were assayed in sand culture pot experiments, totaling four experiments, each for evaluation at V3, V5, V7 and V9 stage, respectively, each in a randomized complete block design with three replications, and each genotype exposed to two Al levels (0 and 480 μM). The relative values of shoot dry weight (RSDW), root dry weight (RRDW), total plant dry weight (RTDW), total root length (RTRL) and total root surface area (RRSA) as the tolerance indicators as well as FAi were compared. All the indicators showed significant variation in Al tolerance among genotypes over and across the leaf stages, but Genotype × Stage interactions were significant only for RTRL and RRSA, indicating that they were less stable among stages than RTDW, RSDW and RRDW. Among the latter three, RTDW was chosen as the major indicator of Al tolerance due to its relatively better stability, higher correlation with other indicators and easier measuring procedure than the others. The seedling age applicable for screening was not definitive, but V5 appeared to compromise between time spent resulting from screening the relatively older seedlings at later stages and low variation among genotypes at a younger stage. The differences of Al tolerance among the tested accessions were further detected by using RTDW, and superior Al tolerant accessions identified were PI.509080 (South Korea), N23533 and N24282 (Northeast China) and PI.159322 (USA), comparable to the putative tolerant check PI.416937 (Japan) at all vegetative stages. © 2010 Higher Education Press and Springer-Verlag Berlin Heidelberg.


Li H.,Nanjing Agricultural University | Li H.,National Center for Soybean Improvement | Li H.,National Key Laboratory for Crop Genetics and Germplasm Enhancement | Zhao T.,Nanjing Agricultural University | And 13 more authors.
Euphytica | Year: 2011

The relative importance of various types of quantitative trait locus (QTL) conferring oil content and its fatty acid components in soybean seeds was assessed through testing a recombinant inbred line (RIL) population (derived from KF1 × NN1138-2) in randomized blocks experiments in 2004-2006. The contents of oil and oleic, linoleic, linolenic, palmitic and stearic acids were determined with automatic Soxhlet extraction system and gas chromatography, respectively. Based on the established genetic linkage map with 834 markers, QTLNetwork2. 0 was used to detect QTL under the genetic model composed of additive, additive × additive (epistasis), additive × year and epistasis × year effects. The contributions to the phenotypic variances of additive QTL and epistatic QTL pairs were 15.7% (3 QTL) and 10.8% (2 pairs) for oil content, 10.4% (3 QTL) and 10.3% (3 pairs) for oleic acid, 11.6% (3 QTL) and 8.5% (2 pairs) for linoleic acid, 28.5% (7 QTL) and 7.6% (3 pairs) for linolenic acid, 27.0% (6 QTL) and 16.6% (7 pairs) for palmitic acid and 29.7% (5 QTL) and 4.3% (1 pair) for stearic acid, respectively. Those of additive QTL by year interaction were small and no epistatic QTL pair by year interaction was found. Among the 27 additive QTL and 36 epistatic QTL (18 pairs), three are duplicated between the two QTL types. A large difference was found between the genotypic variance among RILs and the total variance of mapped QTL, which accounted for 52.9-74.8% of the genotypic variation, much larger than those of additive QTL and epistatic QTL pairs. This part of variance was recognized as that due to a collection of unmapped minor QTL, like polygenes in biometrical genetics, and was designated as collective unmapped minor QTL. The results challenge the breeders for how to pyramid different types of QTL. In addition, the present study supports the mapping strategy of a full model scanning followed by verification with other procedures corresponding to the first results. © 2011 Springer Science+Business Media B.V.

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