Ainong Shi

Genetic structure and diversity of cultivated soybean ( Glycine max (L.) Merr.) landraces in China

The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise Fst values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5°N, 105.4 and 122.2°E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces.

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

Abstract: Cowpea (Vigna unguiculata L. Walp.) is an important legume, and the antioxidant content in cowpea seeds has been recognized as a health-promoting compound for humans. The objectives of this study were to analyze the population structure of cowpea collections and to identify single nucleotide polymorphism (SNP) markers associated with the seed antioxidant content and seed coat colour. A set of 1047 SNPs were used to analyze a 369 cowpea core collection from 47 countries. Results indicated that: (1) there were three clusters in the 369 entries; and the germplasm collected from India, South Africa, and the US showed broader genetic diversity; (2) Scaffold7139_14363 and Scaffold29110_4657 were strongly associated with antioxidant content, and C35063613_1497, Scaffold81493_886, and Scaffold84620_6785 were strongly associated with seed coat colour across three models; (3) significant correlations were detected between the seed antioxidant content and black seed colour (r = 0.45) and between seed antioxidant content and red seed coat colour (r = 0.50); and (4) Scaffold42008_191 and C35082838_2258 were associated with both seed antioxidant content and seed coat colour. The SNP markers identified could potentially be used in marker-assisted breeding to accelerate genetic improvement of cowpea for higher seed antioxidant content.

Yield Potential and Waterlogging Tolerance of Selected Near-Isogenic Lines and Recombinant Inbred Lines from Two Southern Soybean Populations

Abstract A quantitative trait locus (QTL) for waterlogging tolerance has been identified in a northern cultivar Archer. In the current study, Archer was crossed with two southern elite soybean cultivars A5403 and P9641 to investigate the efficiency of marker-assisted selection and phenotypic selection for waterlogging tolerance and to assess the value of waterlogging tolerance for soybean yield improvement. Near-isogenic lines (NILs) were created using the linked simple sequence repeat (SSR) marker Sat_064 for the waterlogging tolerance QTL from each of the F6-derived populations. Concurrently, 103 and 67 recombinant inbred lines (RILs) were also generated from Archer × A5403 and Archer × P9641, respectively. Significant variations in seed yield or plant injury were observed among the NILs and RILs under waterlogging stress. The 29 most tolerant and 29 most sensitive NILs and RILs were selected on the basis of waterlogging injury ratings and evaluated under irrigated and waterlogged conditions in Arkansas and Missouri in 2002 and 2003. The most tolerant lines produced an average of 60.9% of their irrigated yield, as compared with only 32.6% and 53.9% by the most sensitive lines and the commercial checks, respectively. Waterlogging injury scores for the tolerant lines, checks, and sensitive lines were 3.6,4.3, and 6.6, respectively, following the same trend as their yield reductions. A genotype-by-environment interaction (G × E) analysis showed that some of the selected lines were highly stable in response to waterlogging stress across environments. Breeding selection for the waterlogging tolerance can be performed in the field based on seed yield and plant injury scores.

Temperature Affects Expression of Symptoms Induced by Soybean Mosaic Virus in Homozygous and Heterozygous Plants

Seven strains (G1 to G7) of soybean mosaic virus (SMV) and 3 resistance loci (Rsv1, Rsv3, and Rsv4) have been identified in soybean. The interaction of SMV strains and host resistance genes results in resistant (symptomless), susceptible (mosaic), or necrotic (leaf and stem necrosis) reactions. The necrotic reaction may be gene dosage dependent and influenced by temperature. Using a set of soybean isolines and hybrids containing homozygous or heterozygous alleles of rsv, Rsv1, Rsv1-n, Rsv3, or Rsv4, this study has explored the relationship of SMV-induced symptoms and resistance gene dosage at different temperatures. Results showed that SMV-inoculated plants carrying Rsv3 or Rsv4 were symptomless at both homozygous and heterozygous states at all temperature regimes. Threshold temperatures for symptoms changing from stem tip necrosis (STN) to mosaic were 30, 33, and 33 degrees C in G7-inoculated homozygous genotypes V94-3971(Rsv1) and PI 96983 (Rsv1) and G1-inoculated V262 (Rsv1-n), respectively. However, at the heterozygous state, threshold temperature was 30 degrees C in G7-inoculated V94-3971 x Essex F(1) for the symptom change from STN to mosaic, 31 degrees C in G7-inoculated Essex x PI 96983 F(1) from STN to mixture of necrosis and mosaic (N-M), and 32 degrees C in G1-inoculated V262 x Essex F(1) from N-M to mosaic. Incomplete necrosis was observed in the heterozygous state in G1-inoculated V262 x Essex F(1) and G7-inoculated PI 96983 x Essex F(1) where necrotic and mosaic symptoms were mixed. High temperature (37 degrees C) tends to mask the expression of mosaic symptoms in both homozygous and heterozygous plants. STN expression in response to temperature was affected by resistance gene, gene dosage, host genetic background, and specific SMV strains. Thus, Rsv3 and Rsv4 are a better choice as source of genetic resistance for breeding SMV-resistant cultivars.

Irrigation and Planting Date Effects on Seed Yield and Agronomic Traits of Early-Maturing Soybean

ABSTRACT Soybean [Glycine max (L.) Merr.] growers in the mid-south United States have increasingly practiced early planting and double-cropping systems. Information on crop management is desired by soybean growers to improve production and profitability. Effects of irrigation and planting date on seed yield and other agronomic traits were investigated in soybean cultivars from eight maturity groups (MG) in 2002 and 2003 at two locations in Arkansas. The planting date (April, May, and June) and irrigation treatments significantly affected seed yield, plant height, and maturity. Significant effects were also observed for number of nodes, number of pods, and number of seeds per plant, whereas number of branches per plant was not affected by planting date and irrigation treatments. Irrigation improved seed yield by an average of 83% (986 kg/ha) in all experiments conducted across two years. Highest seed yield was achieved when soybeans were planted in May, followed by April and then by June planting. The MG V and VI cultivars, conventionally grown in Arkansas, produced higher seed yields than other maturity groups and were the most suitable cultivar selections when considering seed yield alone. Significant interactions were observed among planting date, irrigation, and maturity groups/genotypes. The MG IV was a better candidate for the double-cropping system (June-planting) because of its earlier maturity and high seed yield. For the early soybean production system (April-planting), MG I and II cultivars were potentially good selections because of their short growing periods and acceptable seed yields. The various planting dates and irrigation systems combined with proper cultivar selections provide soybean producers with more options for using the land and water efficiently.

Genetic Diversity Among Popular Historical Southern U.S. Soybean Cultivars Using AFLP Markers

ABSTRACT Modern soybean [Glycine max (L.) Merr.] breeding extensively uses as crossing parents superior cultivars and breeding lines with locally adapted desirable traits, which may lead to declined genetic diversity and increased frequency of fixed common alleles. The main objective of this research was to evaluate, via amplified fragment length polymorphism (AFLP) markers, the genetic diversity and the genetic relationships among the 38 most popular cultivars and lines in the southern United States. Genetic analysis using AFLP markers with 16 primer combinations revealed an average genetic distance of 0.124 among the 38 genotypes examined. Genetic diversity declined among cultivars released during the 1950s and 1960s compared to those released before the 1950s, but increased in the 1970s and peaked in the 1980s, followed by a decline again in the 1990s and 2000s. While 34 unique bands were identified, allelic frequency analysis revealed 50.8% of the 754 loci examined to be fixed in all 38 genotypes. Future parent selection for crossing should consider using genotypes of greater genetic distance and avoid using lines with common genetic background.

Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from maturity groups IV and V

Phytophthora sojae, an oomycete pathogen of soybean, causes stem and root rot, resulting in annual economic loss up to

Genetic diversity and association analysis of leafminer (Liriomyza langei) resistance in spinach (Spinacia oleracea).

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.

Planting Date and Irrigation Effects on Seed Quality of Early-Maturing Soybean in the Mid-South USA

Leafminer (Liriomyza langei) is a major insect pest of many important agricultural crops, including spinach (Spinacia oleracea). Use of genetic resistance is an efficient, economic, and environment-friendly method to control this pest. The objective of this research was to conduct association analysis and identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance in spinach germplasm. A total of 300 USDA spinach germplasm accessions were used for the association analysis of leafminer resistance. Genotyping by sequencing (GBS) was used for genotyping and 783 SNPs from GBS were used for association analysis. The leafminer resistance showed a near normal distribution with a wide range from 1.1 to 11.7 stings per square centimeter leaf area, suggesting that the leafminer resistance in spinach is a complex trait controlled by multiple genes with minor effect in this spinach panel. Association analysis indicated that five SNP markers, AYZV02040968_7171, AYZV02076752_412, AYZV02098618_4615, AYZV02147304_383, and AYZV02271373_398, were associated with the leafminer resistance with LOD 2.5 or higher. The SNP markers may be useful for breeders to select plants and lines for leafminer resistance in spinach breeding programs through marker-assisted selection.