Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population.

Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log10(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops.

Genome-Wide Association Study of Partial Resistance to P. sojae in Wild Soybeans from Heilongjiang Province, China.

Phytophthora root rot (PRR) is a destructive disease of soybeans (Glycine max (L.) Merr) caused by Phytophthora sojae (P. sojae). The most effective way to prevent the disease is growing resistant or tolerant varieties. Partial resistance provides a more durable resistance against the pathogen compared to complete resistance. Wild soybean (Glycine soja Sieb. & Zucc.) seems to be an extraordinarily important gene pool for soybean improvement due to its high level of genetic variation. In this study, 242 wild soybean germplasms originating from different regions of Heilongjiang province were used to identify resistance genes to P. sojae race 1 using a genome-wide association study (GWAS). A total of nine significant SNPs were detected, repeatedly associated with P. sojae resistance and located on chromosomes 1, 10, 12, 15, 17, 19 and 20. Among them, seven favorable allelic variations associated with P. sojae resistance were evaluated by a t-test. Eight candidate genes were predicted to explore the mechanistic hypotheses of partial resistance, including Glysoja.19G051583, which encodes an LRR receptor-like serine/threonine protein kinase protein, Glysoja.19G051581, which encodes a receptor-like cytosolic serine/threonine protein kinase protein. These findings will provide additional insights into the genetic architecture of P. sojae resistance in a large sample of wild soybeans and P. sojae-resistant breeding through marker-assisted selection.

Identification and expression profiles analysis of odorant-binding proteins in soybean aphid, Aphis glycines (Hemiptera: Aphididae).

The soybean aphid, Aphis glycines, is an extreme specialist and an important invasive pest that relies on olfaction for behaviors such as feeding, mating, and foraging. Odorant-binding proteins (OBPs) play a vital role in olfaction by binding to volatile compounds and by regulating insect sensing of the environment. In this work we used rapid amplification of complementary DNA ends technology to identify and characterize 10 genes encoding A. glycines OBPs (AglyOBPs) belonging to 3 subfamilies, including 4 classic OBPs, 5 Plus-C OBPs, and one Minus-C OBP. Quantitative real-time polymerase chain reaction demonstrated variable specific expression patterns for the 10 genes based on developmental stage and aphid tissue sampled. Expression levels of 7 AglyOBPs (2, 3, 4, 5, 7, 9, and 10) were highest in the 4th instar, indicating that the 4th nymphal instar is an important developmental period during which soybean aphids regulate feeding and search for host plants. Tissue-specific expression results demonstrated that AglyOBP2, 7, and 9 exhibited significantly higher expression levels in antennae. Meanwhile, ligand-binding analysis of 5 OBPs demonstrated binding of AglyOBP2 and AglyOBP3 to a broad spectrum of volatiles released by green leaf plants, with bias toward 6- to 8-carbon chain volatiles and strong binding of AglyOBP7 to trans-ß-farnesene. Taken together, our findings build a foundation of knowledge for use in the study of molecular olfaction mechanisms and provide insights to guide future soybean aphid research.