Dataset Information

Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits.

ABSTRACT: Soybean was domesticated about 5,000 to 6,000 years ago in China. Although genotyping technologies such as genotyping by sequencing (GBS) and high-density array are available, it is convenient and economical to genotype cultivars or populations using medium-density SNP array in genetic study as well as in molecular breeding. In this study, 235 cultivars, collected from China, Japan, USA, Canada and some other countries, were genotyped using SoySNP8k iSelect BeadChip with 7,189 single nucleotide polymorphisms (SNPs). In total, 4,471 polymorphic SNP markers were used to analyze population structure and perform genome-wide association study (GWAS). The most likely K value was 7, indicating this population can be divided into 7 subpopulations, which is well in accordance with the geographic origins of cultivars or accession studied. The LD decay rate was estimated at 184 kb, where r2 dropped to half of its maximum value (0.205). GWAS using FarmCPU detected a stable quantitative trait nucleotide (QTN) for hilum color and seed color, which is consistent with the known loci or genes. Although no universal QTNs for flowering time and maturity were identified across all environments, a total of 30 consistent QTNs were detected for flowering time (R1) or maturity (R7 and R8) on 16 chromosomes, most of them were corresponding to known E1 to E4 genes or QTL region reported in SoyBase (soybase.org). Of 16 consistent QTNs for protein and oil contents, 11 QTNs were detected having antagonistic effects on protein and oil content, while 4 QTNs soly for oil content, and one QTN soly for protein content. The information gained in this study demonstrated that the usefulness of the medium-density SNP array in genotyping for genetic study and molecular breeding.

SUBMITTER: Wang YY

PROVIDER: S-EPMC5954420 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits.

Wang Ya-Ying YY Li Yu-Qiu YQ Wu Hong-Yan HY Hu Bo B Zheng Jia-Jia JJ Zhai Hong H Lv Shi-Xiang SX Liu Xin-Lei XL Chen Xin X Qiu Hong-Mei HM Yang Jiayin J Zong Chun-Mei CM Han De-Zhi DZ Wen Zi-Xiang ZX Wang De-Chun DC Xia Zheng-Jun ZJ

Frontiers in plant science 20180509

Soybean was domesticated about 5,000 to 6,000 years ago in China. Although genotyping technologies such as genotyping by sequencing (GBS) and high-density array are available, it is convenient and economical to genotype cultivars or populations using medium-density SNP array in genetic study as well as in molecular breeding. In this study, 235 cultivars, collected from China, Japan, USA, Canada and some other countries, were genotyped using SoySNP8k iSelect BeadChip with 7,189 single nucleotide ...[more]

PMID: 29868067

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Project description:Soybean (Glycine max) breeding involves improving commercially grown varieties by introgressing important agronomic traits from poor yielding accessions and/or wild relatives of soybean while minimizing the associated yield drag. Molecular markers associated with these traits are instrumental in increasing the efficiency of producing such crosses and Single Nucleotide Polymorphisms (SNPs) are particularly well suited for this task, owing to high density in the non-genic regions and thus increased likelihood of finding a tightly linked marker to a given trait. A rapid method to develop SNP markers that can differentiate specific loci between any two parents in soybean is thus highly desirable. In this study we investigate such a protocol for developing SNP markers between multiple soybean accessions and the reference Williams 82 genome. To restrict sampling frequency reduced representation libraries (RRLs) of genomic DNA were generated by restriction digestion followed by library construction. We chose to sequence four accessions Dowling (PI 548663), Dwight (PI 597386), Komata (PI200492) and PI 594538A for their agronomic importance as well as Williams 82 as a control.MseI was chosen to digest genomic DNA based on predictions that it will cut sparingly in the mathematically defined high-copy-number regions of the genome. All RRLs were sequenced on the Illumina genome analyzer. Reads were aligned to the Glyma1 reference assembly and SNP calls made from the alignments. We identified from 4294 to 14550 SNPs between the four accessions and the Williams 82 reference. In addition a small number of SNPs (1142) were found by aligning Williams 82 reads to the reference assembly (Glyma1) suggesting limited genetic variation within the Williams 82 line. The SNP data allowed us to estimate genetic diversity between the four lines and Williams 82. Restriction digestion of soybean genomic DNA with MseI followed by high throughput sequencing provides a rapid and reproducible method for generating SNP markers.

Project description:To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes encoding storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. More significantly, the power of RNA-Seq to detect genes expressed at low levels revealed hundreds of transcription factors with notable expression in at least one stage of seed development. Results from a second biological replicate demonstrate high reproducibility of these data revealing a comprehensive view of the transciptome of seed development in the cultivar Williams, the reference cultivar for the first soybean genome sequence.

Project description:BackgroundTo continue to meet the increasing demands of soybean worldwide, it is crucial to identify key genes regulating flowering and maturity to expand the cultivated regions into short season areas. Although four soybean genes have been successfully utilized in early maturity breeding programs, new genes governing maturity are continuously being identified suggesting that there remains as yet undiscovered loci governing agronomic traits of interest. The objective of this study was to identify novel loci and genes involved in a diverse set of early soybean maturity using genome-wide association (GWA) analyses to identify loci governing days to maturity (DTM), flowering (DTF) and pod filling (DTPF), as well as yield and 100 seed weight in Canadian environments. To do so, soybean plant introduction lines varying significantly for maturity, but classified as early varieties, were used. Plants were phenotyped for the five agronomic traits for five site-years and GWA approaches used to identify candidate loci and genes affecting each trait.ResultsGenotyping using genotyping-by-sequencing and microarray methods identified 67,594 single nucleotide polymorphisms, of which 31,283 had a linkage disequilibrium < 1 and minor allele frequency > 0.05 and were used for GWA analyses. A total of 9, 6, 4, 5 and 2 loci were detected for GWA analyses for DTM, DTF, DTPF, 100 seed weight and yield, respectively. Regions of interest, including a region surrounding the E1 gene for flowering and maturity, and several novel loci, were identified, with several loci having pleiotropic effects. Novel loci affecting maturity were identified on chromosomes five and 13 and reduced maturity by 7.2 and 3.3 days, respectively. Novel loci for maturity and flowering contained genes orthologous to known Arabidopsis flowering genes, while loci affecting yield and 100 seed weight contained genes known to cause dwarfism.ConclusionsThis study demonstrated substantial variation in soybean agronomic traits of interest, including maturity and flowering dates as well as yield, and the utility of GWA analyses in identifying novel genetic factors underlying important agronomic traits. The loci and candidate genes identified serve as promising targets for future studies examining the mechanisms underlying the related soybean traits.

Project description:The objective of this research was to identify single nucleotide polymorphisms (SNPs) and to develop an Illumina Infinium BeadChip that contained over 50,000 SNPs from soybean (Glycine max L. Merr.). A total of 498,921,777 reads 35-45 bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 of the 209,903 SNPs were determined to be ideal candidates for Illumina Infinium II BeadChip design. To equalize the distance between selected SNPs, increase assay success rate, and minimize the number of SNPs with low minor allele frequency, an iteration algorithm based on a selection index was developed and used to select 60,800 SNPs for Infinium BeadChip design. Of the 60,800 SNPs, 50,701 were targeted to euchromatic regions and 10,000 to heterochromatic regions of the 20 soybean chromosomes. In addition, 99 SNPs were targeted to unanchored sequence scaffolds. Of the 60,800 SNPs, a total of 52,041 passed Illumina's manufacturing phase to produce the SoySNP50K iSelect BeadChip. Validation of the SoySNP50K chip with 96 landrace genotypes, 96 elite cultivars and 96 wild soybean accessions showed that 47,337 SNPs were polymorphic and generated successful SNP allele calls. In addition, 40,841 of the 47,337 SNPs (86%) had minor allele frequencies ≥ 10% among the landraces, elite cultivars and the wild soybean accessions. A total of 620 and 42 candidate regions which may be associated with domestication and recent selection were identified, respectively. The SoySNP50K iSelect SNP beadchip will be a powerful tool for characterizing soybean genetic diversity and linkage disequilibrium, and for constructing high resolution linkage maps to improve the soybean whole genome sequence assembly.

Dataset Information

Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits.

Publications

Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits.

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