Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.

Core Ideas Quantitative trait locus (QTL) mapping for rice yield component traits was conducted in a biparental mapping population whose parents were derived from two diverse tropical japonica accessions included in the Rice Diversity Panel 1 (RDP1). Single nucleotide polymorphisms (SNPs) in QTLs found by genome‐wide association (GWA) studies of the RDP1 for the same yield component traits and located in QTL regions discovered by the biparental mapping population were identified to validate the GWA QTLs. Known candidate genes were located in the biparental QTL regions and near SNPs composing the overlapping GWA QTLs. For biparental QTLs with R2 values above 15.0, we determined if the allele effects in the overlapping GWA QTLs agreed with the biparental QTLs. The Rice Diversity Panel 1 (RDP1) was developed for genome‐wide association (GWA) studies to explore five rice (Oryza sativa L.) subpopulations (indica, aus, aromatic, temperate japonica, and tropical japonica). The RDP1 was evaluated for over 30 traits, including agronomic, panicle architecture, seed, and disease traits and genotyped with 700,000 single nucleotide polymorphisms (SNPs). Most rice grown in the southern United States is tropical japonica and thus the diversity in this subpopulation is interesting to U.S. breeders. Among the RDP1 tropical japonica accessions, ‘Estrela’ and ‘NSFTV199’ are both phenotypically and genotypically diverse, thus making them excellent parents for a biparental mapping population. The objectives were to (i) ascertain the GWA QTLs from the RDP1 GWA studies that overlapped with the QTLs uncovered in an Estrela × NSFTV199 tropical japonica recombinant inbred line (RIL) population evaluated for 15 yield traits, and (ii) identify known or novel genes potentially controlling specific yield component traits. The 256 RILs were genotyped with 132 simple sequence repeat markers and 70 QTLs were found. Perl scripts were developed for automatic identification of the underlying candidate genes in the GWA QTL regions. Approximately 100 GWA QTLs overlapped with 41 Estrela × NSFTV199 QTL (RIL QTL) regions and 47 known genes were identified. Two seed trait RIL QTLs with overlapping GWA QTLs were not associated with a known gene. Segregating SNPs in the overlapping GWA QTLs for RIL QTLs with high R2 values will be evaluated as potential DNA markers useful to breeding programs for the associated yield trait.

Soybean mosaic virus (SMV) is an important viral disease of soybean [Glycine max (L.) Merr.] and causes a drastic reduction of seed yield and quality. Soybean mosaic virus isolates can be classified into one of seven strain groups, G1 through G7. Three loci with SMV resistance alleles Rsv1, Rsv3, and Rsv4 have been reported so far. Each locus contains multiple alleles: nine alleles at Rsv1, three alleles at Rsv3, and two alleles at Rsv4. Soybean cultivars Corsica (PI 559931) and Beeson (PI 548510) exhibit different patterns of response to SMV strains than differential cultivars with known genes. The objective of this study was to investigate the inheritance and allelism of resistance genes in Corsica and Beeson. To examine the inheritance of SMV resistance, Corsica and Beeson were crossed with the susceptible cultivar Essex, and the F2 and F3 progenies were inoculated with a G7 isolate. To identify the allelic relationship of genes in Corsica and Beeson with known SMV resistance loci, they were crossed with PI 96983 (Rsv1), ‘L29’ (Rsv3), and V94‐5152 (Rsv4), and their F2 plants and F2:3 lines were inoculated with G7. A serological tissue blotting immunoassay (TBIA) was used to confirm the presence or absence of the virus in the inoculated plants. Molecular markers were used to confirm the phenotypic data. The results showed a monogenic dominant resistance in Corsica, with the resistant gene located at the Rsv1 locus. Beeson also contains a single dominant gene for SMV resistance, but the gene is located at the Rsv4 locus. Both genes in Corsica and Beeson confer a different SMV reaction pattern than other reported alleles at the same loci. Therefore, we propose the new symbols of Rsv1‐c for the resistant gene in Corsica and Rsv4‐b for the resistant gene in Beeson. The results from the genetic study were confirmed by the molecular markers and TBIA. The information from this study can be used for parent selection by breeders in cross breeding and gene pyramiding.

Species † No. of chromosomes (2n) † Genome † Genome size (Mbp) ‡ Distribution † Section Padia Oryza granulata complex O. granulata Nees et Am. ex Watt 24 GG 862 South and Southeast Asia O. meyeriana (Zoll. et (Mor. ex Steud.) Baill.

Soybean mosaic virus (SMV) is one of the most destructive viral diseases in soybean (Glycine max). Three independent loci for SMV resistance have been identified in soybean germplasm. The use of genetic resistance is the most effective method of controlling this disease. Marker assisted selection (MAS) has become very important and useful in the effort of selecting genes for SMV resistance. Single nucleotide polymorphism (SNP), because of its abundance and high-throughput potential, is a powerful tool in genome mapping, association studies, diversity analysis, and tagging of important genes in plant genomics. In this study, a 10 SNPs plus one insert/deletion (InDel) multiplex assay was developed for SMV resistance: two SNPs were developed from the candidate gene 3gG2 at Rsv1 locus, two SNPs selected from the clone N11PF linked to Rsv1, one 'BARC' SNP screened from soybean chromosome 13 [linkage group (LG) F] near Rsv1, two 'BARC' SNPs from probe A519 linked to Rsv3, one 'BARC' SNP from chromosome 14 (LG B2) near Rsv3, and two 'BARC' SNPs from chromosome 2 (LG D1b) near Rsv4, plus one InDel marker from expressed sequence tag (EST) AW307114 linked to Rsv4. This 11 SNP/InDel multiplex assay showed polymorphism among 47 diverse soybean germplasm, indicating this assay can be used to investigate the mode of inheritance in a SMV resistant soybean line carrying Rsv1, Rsv3, and/or Rsv4 through a segregating population with phenotypic data, and to select a specific gene or pyramid two or three genes for SMV resistance through MAS in soybean breeding program. The presence of two SMV resistance genes (Rsv1 and Rsv3) in J05 soybean was confirmed by the SNP assay.