Association Analysis of Genomic Loci Important for Grain Weight Control in Elite Common Wheat Varieties Cultivated with Variable Water and Fertiliser Supply

Abstract

Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW) in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.

Mining Centuries Old In situ Conserved Turkish Wheat Landraces for Grain Yield and Stripe Rust Resistance Genes

“…The whole genome LD decay rate in the current study (~10 cM; Figure 3) is faster than previously published values in CIMMYT's Elite Spring Wheat materials (~30 cM; Crossa et al, 2007; Dreisigacker et al, 2012) and/or Chinese or European elite germplasm (~20–23 cM; Zhang et al, 2013; Nielsen et al, 2014). However, compared to other wheat global landrace collections (~4–5 cM; Neumann et al, 2011; Adhikari et al, 2012), LD decay rate of the present collection was slower.…”

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

“…At least four genome-wide association mapping studies (GWAS) involving 108-262 genotypes have been conducted in wheat under drought [72][73][74][75], and 60 marker-trait associations (MTAs) were detected for several agronomic and physiological traits. The markers used included genome-wide SSR, SNP, and DArT markers (Table S2).…”

QTL Positioning of Thousand Wheat Grain Weight in Qaidam Basin

“…Without doubt, it might also because they were two different major QTL loci in themselves. A major gene GW2-6A of TGW has been positioned in wheat chromosomes [3] [9]. However, owing to parent differences between different populations and differences among the used molecular markers, it is hard for us to conform whether or not this gene was in the same locus with qTgw6A in this paper.…”

“…Since 1940, TGW of Chinese wheat varieties has increased from the average 31.5 grams in the 1940s to 44.64 grams in 2000, with an addition of 2.19 grams every ten years [2]. At the same time, high TGW can improve the seed germination rate, promote the seedling growth and enhance the variety's ability to resist natural disasters [3]. Furthermore, high TGW can also improve the flour yield and affect the milling quality of wheat grains [4].…”