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

<div><p>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 <i>Xpsp3152</i> frequently co-segregated with the larger grain haplotype of <i>TaGW2-6A</i>, suggesting probable genetic and functional linkages between <i>Xpsp3152</i> and <i>GW2</i> 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.</p> </div

Distribution of the 94 elite common wheat varieties in two-dimensional PCoA space based on the genotyping data of 1,129 molecular markers.

<p>Three groups, I, II and III, were formed, and were dominated by the varieties from Henan, Shandong, and Hebei provinces, respectively. The core breeding parents in the three groups included Abbondanza (Ab), Bima 4 (BM4), Lumai 14 (LM14), Orofen (Of), and St (St2422–464).</p

Assessing potential additive effects among the elite alleles of the associated loci on thousand-grain weight (TGW) (g).

<p>Assessment was carried out for the five loci associated with TGW in environment-independent (EI) manner and for the total number of loci associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), or reduced phosphorus (RP) environments. In each assessment, the 94 varieties were split into two varietal groups differing appropriately in the number of elite alleles. The number of lines (n) in each varietal group is provided in brackets. *and **indicate statistical significance at <i>P</i>≤0.05 and 0.01, respectively. (A) Assessing additive effects among the elite alleles of five EI loci. The highest number of EI elite alleles detected in a single variety was four. Therefore, the 94 varieties were split into two groups, with 0–1 and 2–4 elite alleles of the EI loci, respectively. The average TGW of the varietal group with 2–4 EI elite alleles was generally and significantly higher than that of the group with 0–1 EI elite allele across all 12 environments. (B) Examining additive effects among the elite alleles of the loci associated with TGW in the IF environments. Although the total number of associated loci under IF treatment was nine (including five EI and four IF specific loci), the highest number of elite alleles found in a single variety was only six. Thus, the 94 varieties were divided into two categories, carrying 0–2 and 3–6 elite alleles of the associated loci, respectively. The average TGW of the varietal group with 3–6 elite alleles was generally higher than that of the group with 0–2 elite alleles across the three IF environments. Using the same approach, substantial additive effects were also detected among the elite alleles of the loci associated with TGW under RF, RN, or RP treatments.</p

Phenotypic effects of the 20 chromosomal loci significantly associated with thousand-grain weight (TGW) in EI, ED or SD manners.

1<p>The value in brackets indicates genetic distance (cM) along the given chromosome;</p>2<p>For the microsatellite marker, the size (bp) of the elite allele is given. For the diversity arrays technology (DArT) marker, the elite allele 1 indicates the presence of the locus;</p>3<p>The value in brackets indicates the number of varieties carrying the given elite allele in the association mapping population;</p>4<p>AT, association type; EI, ED and SD refer to environment-independent, environment-dependent, and site-dependent, respectively; IF, RF, RN, and RP indicate irrigated and fertilised, rainfed, reduced nitrogen, and reduced phosphorus treatments, respectively; HS, Hengshui; JY, Jiyuan.</p

Investigation of the genetic relationships among <i>Xpsp3152</i>, <i>Xpsp3071</i>, and <i>TaGW2-6A</i>.

<p>(A) The relative genetic positions of <i>Xpsp3152</i>, <i>Xpsp3071</i>, and <i>TaGW2-6A</i> (indicated by arrows) on chromosome 6A mapped with the DH population of Huapei 3× Yumai 57 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057853#pone.0057853-Zhang3" target="_blank">[70]</a>. The genetic distance (cM) between adjacent markers is shown on the left side of the diagram. (B) Analysis of potential co-segregation between the larger grain haplotype (6A–A) of <i>TaGW2-6A</i> and the elite alleles of <i>Xpsp3152</i> or <i>Xpsp3071</i>. Among the 13 varieties carrying the elite allele of <i>Xpsp3152</i> (Allele 229), 11 had the 6A–A haplotype of <i>TaGW2-6A</i>. By contrast, among the nine varieties with the elite allele of <i>Xpsp3071</i> (Allele 153), only one had the 6A–A haplotype of <i>TaGW2-6A</i>.</p

Phenotypic effects of the loci associated with thousand-grain weight (TGW) in an environment-independent (EI) manner analysed through marker allele-assisted genotyping.

<p>For the diversity arrays technology (DArT) loci (<i>wPt-6965</i> and <i>rPt-1806</i>), the elite alleles (indicated by Allele 1) refer to the presence of their respective DArT sequences. For the microsatellite locus (<i>Xgwm299</i>), the elite allele is represented by the actual size of specific amplicon (Allele 205). The inferior alleles of the DArT and microsatellite loci are indicated by “Allele 0” (reflecting the absence of the DArT sequence) and “others” (additional alleles with amplicon lengths differing from those of the elite alleles), respectively. Compared to the inferior alleles, the elite alleles of <i>wPt-6965</i>, <i>rPt-1806</i> and <i>Xgwm299</i> had generally positive effects on the average TGW (g) across all 12 environments.</p

Positive influence of the elite alleles of 11 significantly associated loci on grain length (GL, mm) and grain width (GW, mm) in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments in the 08/09 wheat crop cycle in Hengshui (HS).

1<p>For the diversity arrays technology (DArT) locus, allele 1 was elite. For the microsatellite locus, the allele labelled with the specific fragment size (bp) was elite; “n” denotes the number of varieties carrying the given allele;</p>2<p>Statistical comparison was made between the averaged measurements of the two allele types. The asterisk and double asterisks indicate <i>P</i>≤0.05 (significant) or 0.01 (highly significant); Statistically significant comparisons are underlined.</p

Linkage disequilibrium (LD, <i>r</i>²) decay plot of 1,129 marker pairs as a function of genetic distance (cM) for the 94 common wheat lines used in this study.

<p>The inset provides a more detailed view of the LD decay characteristics over a 50 cM genetic distance.</p

Phenotypic effects of <i>wPt-2464</i> associated with thousand-grain weight (TGW) (g) at the Hengshui (HS) experimental site analysed through marker allele-assisted genotyping.

<p>The elite and inferior alleles of <i>wPt-2464</i> are represented by “Allele 1” and “Allele 0”, respectively. *and **indicate statistical significance at <i>P</i>≤0.05 and 0.01, respectively. (A) Relative to the inferior allele, the elite allele conferred generally positive effects on the average TGW across the eight HS environments irrespective of cultivation treatment. The number of lines (n) in each varietal group is provided in brackets. (B) Comparisons of the average TGW values of the 25 varieties (carrying <i>wPt-2464</i> elite allele) cultivated in HS or Jiyuan (JY). The average TGWs of these varieties in HS were significantly higher than their corresponding values in JY in the irrigated and fertilised (IF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. But such a difference was not observed in the rainfed (RF) environment.</p