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Zhang Y.,Nanjing Agricultural University | Zhang Y.,National Center for Soybean Improvement | Zhang Y.,Key Laboratory of Biology and Genetic Improvement of Soybean | Zhang Y.,Institute of Agricultural science in Jiangsu Coastal Areas | And 25 more authors.
Journal of Experimental Botany | Year: 2015

A representative sample comprising 366 accessions from the Chinese soybean landrace population (CSLRP) was tested under four growth environments for determination of the whole-genome quantitative trait loci (QTLs) system of the 100-seed weight trait (ranging from 4.59 g to 40.35 g) through genome-wide association study (GWAS). A total of 116 769 single nucleotide polymorphisms (SNPs) were identifed and organized into 29 121 SNP linkage disequilibrium blocks (SNPLDBs) to ft the property of multiple alleles/haplotypes per locus in germplasm. An innovative two-stage GWAS was conducted using a single locus model for shrinking the marker number followed by a multiple loci model utilizing a stepwise regression for the whole-genome QTL identifcation. In total, 98.45% of the phenotypic variance (PV) was accounted for by four large-contribution major QTLs (36.33%), 51 small-contribution major QTLs (43.24%), and a number of unmapped minor QTLs (18.88%), with the QTL×environment variance representing only 1.01% of the PV. The allele numbers of each QTL ranged from two to 10. A total of 263 alleles along with the respective allele effects were estimated and organized into a 263 × 366 matrix, giving the compact genetic constitution of the CSLRP. Differentiations among the ecoregion matrices were found. No landrace had alleles which were all positive or all negative, indicating a hidden potential for recombination. The optimal crosses within and among ecoregions were predicted, and showed great transgressive potential. From the QTL system, 39 candidate genes were annotated, of which 26 were involved with the gene ontology categories of biological process, cellular component, and molecular function, indicating that diverse genes are involved in directing the 100-seed weight. © 2015 The Author. Published by Oxford University Press on behalf of the Society for Experimental Biology. Source

He J.,Nanjing Agricultural University | He J.,National Center for Soybean Improvement | He J.,Key Laboratory of Biology and Genetic Improvement of Soybean | Li J.,Nanjing Agricultural University | And 13 more authors.
PLoS ONE | Year: 2015

Experimental error control is very important in quantitative trait locus (QTL) mapping. Although numerous statistical methods have been developed for QTL mapping, a QTL detection model based on an appropriate experimental design that emphasizes error control has not been developed. Lattice design is very suitable for experiments with large sample sizes, which is usually required for accurate mapping of quantitative traits. However, the lack of a QTL mapping method based on lattice design dictates that the arithmetic mean or adjusted mean of each line of observations in the lattice design had to be used as a response variable, resulting in low QTL detection power. As an improvement, we developed a QTL mapping method termed composite interval mapping based on lattice design (CIMLD). In the lattice design, experimental errors are decomposed into random errors and block-within-replication errors. Four levels of block-within-replication errors were simulated to show the power of QTL detection under different error controls. The simulation results showed that the arithmetic mean method, which is equivalent to a method under random complete block design (RCBD), was very sensitive to the size of the block variance and with the increase of block variance, the power of QTL detection decreased from 51.3% to 9.4%. In contrast to the RCBD method, the power of CIMLD and the adjusted mean method did not change for different block variances. The CIMLD method showed 1.2- to 7.6-fold higher power of QTL detection than the arithmetic or adjusted mean methods. Our proposed method was applied to real soybean (Glycine max) data as an example and 10 QTLs for biomass were identified that explained 65.87% of the phenotypic variation, while only three and two QTLs were identified by arithmetic and adjusted mean methods, respectively. © 2015 He et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

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. Source

Meng S.,Nanjing Agricultural University | Meng S.,National Center for Soybean Improvement | He J.,Nanjing Agricultural University | He J.,National Center for Soybean Improvement | And 19 more authors.
Theoretical and Applied Genetics | Year: 2016

Key message: Utilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation.Abstract: The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ2-tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTL-allele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs. © 2016 Springer-Verlag Berlin Heidelberg Source

Wang W.,Nanjing Agricultural University | Wang W.,National Center for Soybean Improvement | Wang W.,Key Laboratory of Biology and Genetic Improvement of Soybean | Li X.,Nanjing Agricultural University | And 14 more authors.
Euphytica | Year: 2016

Glycine soja has the potential to improve upon the cultivated soybean (G. max) in protein content, resistance/tolerance to stresses, and other traits, but its small 100-seed weight (100SW) is usually undesired. To explore the 100SW QTL-allele system of G. soja, the recombinant inbred line population NJRINY with 286 lines was developed from a cross between G. max (NN86-4, 17.9 g) and G. soja (PI342618B, 1.1 g) and was tested over 4 years. The genetic linkage map was constructed with 181 PAV (presence/absence variation) and 42 SSR markers. The quantitative trait locus (QTL) mapping results showed that the wild genetic system of 100SW was composed of three groups of QTLs, including (1) 15 additive QTLs, which accounted for 55.1 % of the phenotypic variation (PV), with each locus contributing 1.5–8.1 % of the PV and all of the wild alleles having negative effects (−0.1 to −0.5 g); (2) 17 epistatic QTL pairs, which accounted for 19.0 % of the PV, with epistatic effects positive for parental type (0.1–0.2 g) and negative for recombinants and all of the QTLs in epistatic pairs having simultaneously additive effects except one pair (SW16); (3) a collection of unmapped minor QTLs that accounted for 22.9 % of the PV. Among the detected total additive and/or epistatic QTLs, 12 QTLs have been reported in the literature, but five of the QTLs and all of the epistatic pairs have not been reported before. The results can be used for marker-assisted breeding for 100SW. © 2015, Springer Science+Business Media Dordrecht. Source

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