Browsing by Author "Song, Qijian"

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    Determining Genetic Markers and Seed Compositions Related to High Test Weight in Glycine max
    Shea, Zachary; Singer, William M.; Rosso, Luciana; Song, Qijian; Zhang, Bo (MDPI, 2023-08-19)
    Test weight, one of the primary indicators of soybean seed quality, is measured as the amount of soybean seeds in kilograms that can fit into one hectoliter. The price that growers receive for their soybean is dependent on test weight. Over the past 50 years, growers have observed a decreasing trend in test weight. Therefore, it is imperative to understand better the relationship between soybean test weight and other traits to enable breeders to select parental lines with high test weights in breeding programs to ensure the grower’s profitability. The objectives of the study were to identify genetic markers associated with high test weight in soybean and to determine the correlation between high test weight and five important seed composition traits (protein, oil, sucrose, raffinose, and stachyose content). Maturity group IV and V germplasms from the USDA soybean germplasm collection were grown in Blacksburg and Warsaw in Virginia from 2019 to 2021 and were measured for all of the above traits. Results show that test weight values ranged from 62–77 kg/hL over the three years. Multiple single-nucleotide polymorphisms (SNPs) significantly associated with high test weight were found on chromosome (Chr.) 15 along with a couple on chromosome 14, and 11 candidate genes were found near these SNPs. Test weight was found to be significantly negatively correlated with oil content, inconsistently correlated with protein content in all environments, and negatively correlated but not significantly with all three sugars except for raffinose in Blacksburg 2019. We concluded that the genes that underlie test weight might be on chromosome 15, and the validated associated SNPs might be used to assist breeding selection of test weight. Breeders should pay special attention to test weight while selecting for high oil content in soybean due to their negative correlation.
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    Development of Breeder-Friendly KASP Markers for Low Concentration of Kunitz Trypsin Inhibitor in Soybean Seeds
    Rosso, M. Luciana; Shang, Chao; Song, Qijian; Escamilla, Diana M.; Gillenwater, Jay; Zhang, Bo (MDPI, 2021-03-06)
    Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals’ protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds.
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    Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds
    Qin, Jun; Shi, Ainong; Song, Qijian; Li, Song; Wang, Fengmin; Cao, Yinghao; Ravelombola, Waltram; Song, Qi; Yang, Chunyan; Zhang, Mengchen (2019-11-15)
    Soybean is a major source of protein for human consumption and animal feed. Releasing new cultivars with high nutritional value is one of the major goals in soybean breeding. To achieve this goal, genome-wide association studies of seed amino acid contents were conducted based on 249 soybean accessions from China, US, Japan, and South Korea. The accessions were evaluated for 15 amino acids and genotyped by sequencing. Significant genetic variation was observed for amino acids among the accessions. Among the 231 single nucleotide polymorphisms (SNPs) significantly associated with variations in amino acid contents, fifteen SNPs localized near 14 candidate genes involving in amino acid metabolism. The amino acids were classified into two groups with five in one group and seven amino acids in the other. Correlation coefficients among the amino acids within each group were high and positive, but the correlation coefficients of amino acids between the two groups were negative. Twenty-five SNP markers associated with multiple amino acids can be used to simultaneously improve multi-amino acid concentration in soybean. Genomic selection analysis of amino acid concentration showed that selection efficiency of amino acids based on the markers significantly associated with all 15 amino acids was higher than that based on random markers or markers only associated with individual amino acid. The identified markers could facilitate selection of soybean varieties with improved seed quality.
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    Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from maturity groups IV and V
    Qin, Jun; Song, Qijian; Shi, Ainong; Li, Song; Zhang, Mengchen; Zhang, Bo (PLOS, 2017-09-14)
    Phytophthora sojae, an oomycete pathogen of soybean, causes stem and root rot, resulting in annual economic loss up to $2 billion worldwide. Varieties with P. sojae resistance are environmental friendly to effectively reduce disease damages. In order to improve the resistance of P. sojae and broaden the genetic diversity in Southern soybean cultivars and germplasm in the U.S., we established a P. sojae resistance gene pool that has high genetic diversity, and explored genomic regions underlying the host resistance to P. sojae races 1, 3, 7, 17 and 25. A soybean germplasm panel from maturity groups (MGs) IV and V including 189 accessions originated from 10 countries were used in this study. The panel had a high genetic diversity compared to the 6,749 accessions from MGs IV and V in USDA Soybean Germplasm Collection. Based on disease evaluation dataset of these accessions inoculated with P. sojae races 1, 3, 7, 17 and 25, which are publically available, five accessions in this panel were resistant to all races. Genome-wide association analysis identified a total of 32 significant SNPs, which were clustered in resistance-associated genomic regions, among those, ss715619920 was only 3kb away from the gene Glyma. 14g087500, a subtilisin protease. Gene expression analysis showed that the gene was down-regulated more than 4 fold (log2 fold > 2.2) in response to P. sojae infection. The identified molecular markers and genomic regions that are associated with the disease resistance in this gene pool will greatly assist the U.S. Southern soybean breeders in developing elite varieties with broad genetic background and P. sojae resistance.
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    Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine maxL.)
    Zhu, Qian; Escamilla, Diana M.; Wu, Xingbo; Song, Qijian; Li, Song; Rosso, M. Luciana; Lord, Nilanka; Xie, Futi; Zhang, Bo (2020-11)
    Key message Two major QTLs associated with low seed coat deficiency of soybean seeds were identified in two biparental populations, and three SNP markers were validated to assist low-SCD natto soybean breeding selection. Soybean seed coat deficiency (SCD), known as seed coat cracking during soaking in the natto production process, is problematic because split or broken beans clog production lines and increases production costs. Development of natto soybean cultivars with low SCD is crucial to support the growth of the natto industry. Unfortunately, information on the genetic control of SCD in soybean, which is desperately needed to facilitate breeding selection, remains sparse. In this study, two F(2)populations derived from V11-0883 x V12-1626 (Pop 1) and V11-0883 x V12-1885 (Pop 2) were developed and genotyped with BARCSoySNP6K Beadchips and F-2-derived lines were evaluated for SCD in three consecutive years (2016-2018) in order to identify quantitative trait loci (QTLs) associated with low SCD in soybean. A total of 17 QTLs underlying SCD were identified in two populations. Among these, two major and stable QTLs,qSCD15on chromosome 15 andqSCD20on chromosome 20, were detected across multiple years. These QTLs explained up to 30.3% of the phenotypic variation for SCD in Pop 1 and 6.1% in Pop 2 across years. Three SNP markers associated with theqSCD20were validated in additional four biparental populations. The average selection efficiency of low-SCD soybean was 77% based on two tightly linked markers, Gm20_34626867 and Gm20_34942502, and 64% based on the marker Gm20_35625615. The novel and stable QTLs identified in this study will facilitate elucidation of the genetic mechanism controlling SCD in soybean, and the markers will significantly accelerate breeding for low-SCD soybean through marker-assisted selection.
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    Identification of Quantitative Disease Resistance Loci Toward Four Pythium Species in Soybean
    Clevinger, Elizabeth M.; Biyashev, Ruslan M.; Lerch-Olson, Elizabeth; Yu, Haipeng; Quigley, Charles; Song, Qijian; Dorrance, Anne E.; Robertson, Alison E.; Saghai-Maroof, Mohammad A. (Frontiers, 2021-03-30)
    In this study, four recombinant inbred line (RIL) soybean populations were screened for their response to infection by Pythium sylvaticum, Pythium irregulare, Pythium oopapillum, and Pythium torulosum. The parents, PI 424237A, PI 424237B, PI 408097, and PI 408029, had higher levels of resistance to these species in a preliminary screening and were crossed with “Williams,” a susceptible cultivar. A modified seed rot assay was used to evaluate RIL populations for their response to specific Pythium species selected for a particular population based on preliminary screenings. Over 2500 single-nucleotide polymorphism (SNP) markers were used to construct chromosomal maps to identify regions associated with resistance to Pythium species. Several minor and large effect quantitative disease resistance loci (QDRL) were identified including one large effect QDRL on chromosome 8 in the population of PI 408097 × Williams. It was identified by two different disease reaction traits in P. sylvaticum, P. irregulare, and P. torulosum. Another large effect QDRL was identified on chromosome 6 in the population of PI 408029 × Williams, and conferred resistance to P. sylvaticum and P. irregulare. These large effect QDRL will contribute toward the development of improved soybean cultivars with higher levels of resistance to these common soil-borne pathogens.
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    Improving Breeding Selection of Seed Quality Traits for Food-Grade Soybeans
    Escamilla Sanchez, Diana Marcela (Virginia Tech, 2018-01-29)
    Natto and sprout soybeans are produced using small-seeded soybeans and their production is a high value alternative to grow grain soybeans for food in U.S. The development of soybean cultivars with improved natto and sprout quality is crucial for maintaining and increasing the soyfood market. However, there is insufficient information on sprout soybean characteristics. Therefore, the first objective of this study was to evaluate seed and sprout traits as potential selection criteria and study the storage effect on sprout quality. Seeds can be a vehicle for transmission of pathogens capable of causing human illness. That is why, the second objective was to identify seed-borne pathogens on a commercial soybean cultivar and to evaluate different seed decontamination treatments. Finally, seed coat deficiency is an undesirable trait for natto soybean seeds because it causes inferior appearance of the product. Thus, the third objective was to identify quantitative trait loci (QTL) underlying seed coat deficiency (SCD) and associated markers. Results showed that seed size, high-, average- and low-quality sprout percentage, hypocotyl thickness and length and sprout yield are the most important variables for breeding sprout cultivars; and one-year seed storage at room temperature reduced sprout quality. Fusarium, Alternaria and Diaphorte were the most frequent genera isolated from soybean seeds, and 2% calcium hypochlorite and 5% acetic acid were promising seed disinfection treatments. A stable QTL, qSCD20_1, was identified across two years explaining up to 25% of the variation of SCD; and eight molecular markers tightly linked and nearby qSCD20_1 were identified. Information presented will be helpful for sprout and natto soybean cultivar development.