Association Mapping and Nucleotide Sequence Variation in Five Drought Tolerance Candidate Genes in Spring Wheat

Abstract

Functional markers are needed for key genes involved in drought tolerance to improve selection for crop yield under moisture stress conditions. The objectives of this study were to (i) characterize five drought tolerance candidate genes, namely dehydration responsive element binding 1A (DREB1A), enhanced response to abscisic acid (ERA1‐B and ERA1‐D), and fructan 1‐exohydrolase (1‐FEH‐A and 1‐FEH‐B), in wheat (Triticum aestivum L.) for nucleotide and haplotype diversity, Tajima's D value, and linkage disequilibrium (LD) and (ii) associate within‐gene single nucleotide polymorphisms (SNPs) with phenotypic traits in a spring wheat association mapping panel (n = 126). Field trials were grown under contrasting moisture regimes in Greeley, CO, and Melkassa, Ethiopia, in 2010 and 2011. Genome‐specific amplification and DNA sequence analysis of the genes identified SNPs and revealed differences in nucleotide and haplotype diversity, Tajima's D, and patterns of LD. DREB1A showed associations (false discovery rate adjusted probability value = 0.1) with normalized difference vegetation index, heading date, biomass, and spikelet number. Both ERA1‐A and ERA1‐B were associated with harvest index, flag leaf width, and leaf senescence. 1‐FEH‐A was associated with grain yield, and 1‐FEH‐B was associated with thousand kernel weight and test weight. If validated in relevant genetic backgrounds, the identified marker–trait associations may be applied to functional marker‐assisted selection.

QTL Analysis for Drought Tolerance in Wheat: Present Status and Future Possibilities

“…Besides GWAS, candidate gene-based association mapping involving the following five genes that are involved in drought tolerance in wheat have also been carried out [76]: (i) DREB1A (dehydration responsive element binding); (ii) 1-FEH-A and 1-FEH-B, each for fructan-exohydrolase; and (iii) ERA1-B and ERA1-D, each for enhanced response to abscisic acid (ABA). Sequence variation of the genes was examined in a spring wheat association mapping panel consisting of 126 genotypes.…”

Functional molecular markers for crop improvement

“…These identified marker-trait associations (MTA) may be applied to functional marker-assisted selection, following validation in relevant genetic backgrounds. Several SNPs in drought tolerant candidate genes showed association with yield related and morphological traits in wheat (Edae et al, 2013). Combined linkage and candidate gene based association mapping of the Scmv1 (Sugar cane mosaic virus) locus in maize pinpointed Zmtrx as the most likely positional candidate gene for Scmv1 resistance, and two SNPs identified in this gene were associated with SCMV resistance (Tao et al, 2013).…”

Expression profiling and sequence diversity of novel DREB genes from common bean (Phaseolus vulgaris L.) and their association with drought-related traits

“…As an alternative to the traditional linkage maps, association mapping offers three main advantages, according to Yu and Buckler (2006 (EDAE et al, 2013).…”

“…DREB genes have been extensively characterized in Arabidopsis , rice ), soybean (ZHANG et al, 2008MARCOLINO-GOMES et al, 2013) and several other species. Nucleotide polymorphisms have been found associated with specific traits such as with root dry weight and yield under drought and heat stress in chickpea , plant biomass in wheat (EDAE et al, 2013), relative water content in foxtail millet , yield in rice (SELLAMMAL et al, 2013). In common bean, only one work attempted to associate nucleotide patterns of two DREB loci with drought-tolerance levels .…”

“…Furthermore, similar analyses were performed in wheat, including a DREB1 gene as the candidate. In total, 126 lines were phenotyped and genotyped, and a significant association was detected between biomass and DREB1 (EDAE et al, 2013). …”