Whole Genome Association Mapping of Plant Height in Winter Wheat (Triticum aestivum L.)

Abstract

The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (−log10 (P-value) ≥4.82) and 280 (−log10 (P-value) ≥5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development.

Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.)

“…Numerous studies exhibited that there were major QTL/genes on chromosome 2DS, such as the well-known and widely used dwarf gene Rht8 (Chebotar et al 2013; Griffiths et al 2012; Zanke et al 2014). Recently, using a fine-resolution mapping approach, the Rht8 genetic interval has been reduced from 20.5 to 1.29 cM, flanking by DG279 and DG371 (Gasperini et al 2012).…”

“…Over the past two decades, the successful application of quantitative–genetic methodology has facilitated identification of numerous QTL for PHT in wheat (Borner et al 2002; Cadalen et al 1998; Wurschum et al 2015, 2017; Yu et al 2014; Zanke et al 2014). In our recent study, two QTL ( QPht.cau - 2D.1 and QPht.cau - 2D.2 ) for PHT linked in coupling phase were mapped on the short arm of chromosome 2D (Zhai et al 2016).…”

High‐density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

“…Several MTAs for agronomic traits were detected, including new loci. We identified several MTAs for PH, a trait of renowned complexity in wheat (Maccaferri et al ., ; Zanke et al ., ). At FDR 5%, we identified MTAs on Chr 1B (19.4 and 23.2 cM), 2A (154.6 cM), 3B (166 cM), 4A (114.6 cM), 4B (14.4 cM), 6B (71.9 and 155.1 cM) and 7B (92 cM).…”

“…The map position reported for GA20ox1 and KAO‐B1 makes them candidates for our MTA on Chr 4A. Rht13 co‐localizes with the MTA on Chr 7B (Zanke et al ., ). It should be noted that the majority of studies conducted up to now have focused on bread wheat, and that durum wheat might show a different composition for these complex traits.…”

QTL mapping of Fusarium head blight resistance in three related durum wheat populations

“…In the SD population, the two additional QTL on 4AL and 6AS exerted at the same time strong effect on plant height and FHB resistance. The QTL on 4AL mapped to a similar region as a QTL associated with PH in hexaploid wheat corresponding to a kaurenoic acid oxidase (KAO) gene (Khlestkina et al 2010; Zanke et al 2014), while reduced height genes have been reported on 6AS in durum wheat (Haque et al 2011). These genes are gibberellin-sensitive and not comparable to Rht - B1 in that aspect.…”