Pengyin Chen

Molecular mapping and genomics of soybean seed protein: a review and perspective for the future

Key messageGenetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches.AbstractMeal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content’s negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.

A major natural genetic variation associated with root system architecture and plasticity improves waterlogging tolerance and yield in soybean: Waterlogging tolerance and root system plasticity in soybean

Natural genetic variations in waterlogging tolerance are controlled by multiple genes mapped as quantitative trait loci (QTLs) in major crops, including soybean (Glycine max L.). In this research, 2 novel QTLs associated with waterlogging tolerance were mapped from an elite/exotic soybean cross. The subsequent research was focused on a major QTL (qWT_Gm03) with the tolerant allele from the exotic parent. This QTL was isolated into near-isogenic backgrounds, and its effects on waterlogging tolerance were validated in multiple environments. Fine mapping narrowed qWT_Gm03 into a genomic region of <380xa0Kbp excluding Rps1 gene for Phytophthora sojae resistance. The tolerant allele of qWT_Gm03 promotes root growth under nonstress conditions and favourable root plasticity under waterlogging, resulting in improved waterlogging tolerance, yield, and drought tolerance-related traits, possibly through more efficient water/nutrient uptakes. Meanwhile, involvement of auxin pathways was also identified in the regulation of waterlogging tolerance, as the genotypic differences of qWT_Gm03 in waterlogging tolerance and formation of adventitious/aerial roots can be complemented by an exogenous auxin-biosynthesis inhibitor. These findings provided genetic resources to address the urgent demand of improving waterlogging tolerance in soybean and revealed the determinant roles of root architecture and plasticity in the plant adaptation to waterlogging.

Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages

Key messageThis is the first report on association analysis of salt tolerance and identification of SNP markers associated with salt tolerance in cowpea.AbstractCowpea (Vigna unguiculata (L.) Walp) is one of the most important cultivated legumes in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetic underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt-tolerant cowpea cultivars. The objectives of this study were to conduct association mapping for salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. We analyzed the salt tolerance index of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1049 SNPs postulated from genotyping-by-sequencing were used for association analysis. Population structure was inferred using Structurexa02.3.4; K optimal was determined using Structure Harvester. TASSEL 5, GAPIT, and FarmCPU involving three models such as single marker regression, general linear model, and mixed linear model were used for the association study. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were structured into two subpopulations. Three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage. Seven SNPs, Scaffold93827_270, Scaffold68489_600, Scaffold87490_633, Scaffold87490_640, Scaffold82042_3387, C35069468_1916, and Scaffold93942_1089 were found to be associated with salt tolerance at seedling stage. The SNP markers were consistent across the three models and could be used as a tool to select salt-tolerant lines for breeding improved cowpea tolerance to salinity.

Advances in Genetics and Breeding of Salt Tolerance in Soybean

Salt stress is one of the major abiotic factors affecting crop growth and production. In general, soybean is sensitive to salt stress. The success of soybean improvement for salt tolerance depends on discovery and utilization of genetic variation in the germplasm. In this chapter, advance in salt-tolerant research and breeding was summarized by highlighting the genetic diversity, quantitative trait loci (QTL), identification of the major locus (Glyma03g32900), and improvement of soybean varieties in salt tolerance. The ion exclusion and tissue tolerance mechanisms regulated by this major locus are discussed. In addition, genomic resources and high-throughput phenotyping platforms that can facilitate a better understanding of phenotype-genotype association and formulate genomic-assisted breeding strategies are prospected.

RNA sequencing analysis of salt tolerance in soybean (Glycine max)

Salt stress causes foliar chlorosis and scorch, plant stunting, and eventually yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanisms for salt tolerance is complex and not clear yet. Based on the results from the screening of the RA-452 x Osage mapping population, two F4:6 lines with extreme responses, most tolerant and most sensitive, were selected for a time-course gene expression study in which the 250u202fmM NaCl treatment was initially imposed at the V1 stage and continued for 24u202fh (hrs). Total RNA was isolated from the leaves harvested at 0, 6, 12, 24u202fh after the initiation of salt treatment, respectively. The RNA-Seq analysis was conducted to compare the salt tolerant genotype with salt sensitive genotype at each time point using RNA-Seq pipeline method. A total of 2374, 998, 1746, and 630 differentially expressed genes (DEGs) between salt-tolerant line and salt-sensitive line, were found at 0, 6, 12, and 24u202fh, respectively. The expression patterns of 154 common DEGs among all the time points were investigated, of which, six common DEGs were upregulated and seven common DEGs were downregulated in salt-tolerant line. Moreover, 13 common DEGs were dramatically expressed at all the time points. Based on Log2 (fold change) of expression level of salt-tolerant line to salt-sensitive line and gene annotation, Glyma.02G228100, Glyma.03G226000, Glyma.03G031000, Glyma.03G031400, Glyma.04G180300, Glyma.04G180400, Glyma.05u202fg204600, Glyma.08G189600, Glyma.13G042200, and Glyma.17G173200, were considered to be the key potential genes involving in the salt-tolerance mechanism in the soybean salt-tolerant line.