Background Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. Typically, GWAS in crops are performed using a panel of inbred lines, where multiple replicates of the same inbred are measured and the average phenotype is taken as the response variable. Here we describe and evaluate single plant GWAS (sp-GWAS) for performing a GWAS on individual plants, which does not require an association panel of inbreds. Instead sp-GWAS relies on the phenotypes and genotypes from individual plants sampled from a randomly mating population. Importantly, we demonstrate how sp-GWAS can be efficiently combined with a bulk segregant analysis (BSA) experiment to rapidly corroborate evidence for significant SNPs. Results In this study we used the Shoepeg maize landrace, collected as an open pollinating variety from a farm in Southern Missouri in the 1960’s, to evaluate whether sp-GWAS coupled with BSA can efficiently and powerfully used to detect significant association of SNPs for plant height (PH). Plant were grown in 8 locations across two years and in total 768 individuals were genotyped and phenotyped for sp-GWAS. A total of 306 k polymorphic markers in 768 individuals evaluated via association analysis detected 25 significant SNPs (P ≤ 0.00001) for PH. The results from our single-plant GWAS were further validated by bulk segregant analysis (BSA) for PH. BSA sequencing was performed on the same population by selecting tall and short plants as separate bulks. This approach identified 37 genomic regions for plant height. Of the 25 significant SNPs from GWAS, the three most significant SNPs co-localize with regions identified by BSA. Conclusion Overall, this study demonstrates that sp-GWAS coupled with BSA can be a useful tool for detecting significant SNPs and identifying candidate genes. This result is particularly useful for species/populations where association panels are not readily available.
The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41, and hk5. These findings provide a foundation for enhanced understanding of RPR and the improvement of stalk lodging resistance.
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.
Stalk lodging, breakage of the stalk at or below the ear, causes substantial yield losses in maize. The strength of the stalk rind, commonly measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance RPR genetic architecture, we conducted selection mapping on populations developed by 15 cycles of divergent selection for high (C15-H) and low (C15-L) RPR. We also performed time-course transcriptome and metabolic analyses on developing stalks of high (Hrpr1) and low (Lrpr1) RPR inbred lines derived from the C15-H and C15-L populations, respectively. Divergent selection significantly altered allele frequencies at 3,656 and 3,412 single nucleotide polymorphisms (SNP) in the C15-H and C15-L populations, respectively. While the majority of the SNPs under selection were unique, 110 SNPs were common in both populations indicating the fixation of alleles with alternative effects. Remarkably, preferential selection on the genomic regions associated with lignin and polysaccharide biosynthesis genes was observed in C15-H and C15-L populations, respectively. This observation was supported by higher lignification and lower extractability of cell wall-bound sugars in Hrpr1 compared to Lrpr1. Tricin, a monolignol important for incorporation of lignin in grass cell walls, emerged as a key determinant of the different cell wall properties of Hrpr1 and Lrpr1. Integration of selection mapping with transcriptomics and previous genetic studies on RPR identified 40 novel candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, two PAL paralogues, two lichenases, ZmEXPA2, ZmIAA41, and Caleosin. Enhanced mechanistic and genetic understanding of RPR provides a foundation for improved stalk lodging resistance.
‘GEMS‐0067’ is a maize (Zea mays L.) cultivar that is uniquely high in the proportion of amylose endosperm starch relative to amylopectin. We previously identified a significant quantitative trait locus (QTL) for endosperm amylose content on the short arm of chromosome 5 (5S). In that study, both parental lines, GEMS‐0067 and H99ae, were homozygous recessive for amylose extender 1 (ae1), which is located on the long arm of chromosome 5 (5L). The dominant allele encodes starch branching enzyme 2b (SBE2b). Centered within the 5S QTL interval is another starch branching enzyme, starch branching enzyme 1 (sbe1), which also plays a role in the branching of amylopectin. We sought to determine if this QTL is due to allelic segregation of sbe1 or, instead, a closely linked locus. A Mutator‐induced allele of sbe1 (sbe1‐Mu) was employed to address this question. If sbe1‐Mu behaves as a simple recessive allele, it could eliminate the additive nature of the 5S QTL, which would indicate that segregation of the sbe1 alleles present in the original GEMS‐0067 × H99ae hybrid are responsible for the QTL. If not, it would implicate segregation of alleles at a closely linked locus. Pollen possessing sbe1‐Mu was crossed onto a GEMS‐0067 × H99ae hybrid, which separated the high amylose factor from the low amylose factor. A sample of these progeny was grown and self‐pollinated to generate kernels segregating for sbe1‐Mu. Kernels were genotyped for sbe1 alleles and assayed for relative amylose and amylopectin content. Kernels heterozygous or homozygous for the GEMS‐0067 allele of sbe1 had a higher amylose/amylopectin ratio than kernels possessing the H99ae allele. Importantly, sbe1‐Mu behaves as a simple recessive allele regardless of the other sbe1 allele. This implicates allelic variation of sbe1 as being responsible for the high endosperm amylose QTL.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.