Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat

Abstract

Photoperiod response in wheat is determined to a large extent by the homoeologous series of Photoperiod 1 (Ppd1) genes. In this study, Ppd-A1 genomic sequences from the 5' UTR and promoter region were analysed in 104 accessions of six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and 102 accessions of six hexaploid wheat species (T. aestivum, T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii). This data was supplemented with in silico analysis of publicly available sequences from 46 to 193 accessions of diploid and tetraploid wheat, respectively. Analysis of a region of the Ppd-A1 promoter identified thirteen haplotypes, which were divided in two haplogroups. Distribution of the Ppd-A1 haplogroups and haplotypes in wheat species, and their geographical distributions were analysed. Polymerase chain reaction combined with a heteroduplex mobility assay was subsequently used to efficiently discriminate between Ppd-A1 alleles, allowing identification of the Ppd-A1b haplotypes and haplogroups. The causes of anomalous migration of Ppd-A1 heteroduplexes in gels were found to be the localization of mismatches relative to the center of fragment, the cumulative effect of neighbouring polymorphic sites, and the location of mismatches within A/T-tracts. Analysis of the Ppd-A1 5' UTR in hexaploid wheat revealed a novel mutation within the "photoperiod critical" region in a subset of T. compactum accessions. This putative photoperiod insensitive allele (designated Ppd-A1a.4) includes a 684 bp deletion which spans region in common with deletions previously identified in other photoperiod insensitive Ppd1 alleles.

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

“…By understanding the haplotypes available within elite cultivars, we can also use a prospective approach to mine landrace and wild relative collections for novel haplotypes. This approach could entail mining for haplotypes that break negative correlations across specific low‐recombinogenic regions (Winfield et al ., ), or alternatively mining for novel haplotypes across QTL loci associated with a known agronomic trait (Muterko et al ., ). This will become more commonplace as large diversity collections are genotyped at high‐density and haplotype imputation becomes more robust (Jordan et al ., ).…”

Wheat pre-anthesis development as affected by photoperiod sensitivity genes (Ppd-1) under contrasting photoperiods

“…Sources of variation in the ranking mentioned -beyond the stated above-could be different alleles for a given locus, i.e. the functional polymorphism in Ppd-B1 (Tanio and Kato 2007;Nishida et al 2013) or copy number variation in Ppd-B1 as well (Beales et al 2007;Bentley et al 2011;Díaz et al 2012;Shaw et al 2012;Nishida et al 2013;Muterko et al 2015;Matsuyama et al 2015). Ochagavía et al (2017) grew a more comprehensive collection of NILs in the field and in general found similar, though not identical, results on the effects on developmental phases, revealing again that any ranking on effects would be susceptible to the combination of genetic (e.g.…”

High Frequency of Doubled Haploid Plant Production in Spelt Wheat

“…The importance of spelt wheat is increasing not only in organic farming but also in basic and applied research (Dvorak et al, 2012;Muterko et al, 2015;Zuk-Golaszewska et al, 2015). Spelt wheat germplasm offers excellent genetic resources for improving biotic and abiotic stress tolerance in common wheat (Triticum aestivum L.).…”