Molecular characterization of vernalization and response genes in bread wheat from the Yellow and Huai Valley of China

Abstract

BackgroundFlowering time greatly influences the adaptation of wheat cultivars to diverse environmental conditions and is mainly controlled by vernalization and photoperiod genes. In wheat cultivars from the Yellow and Huai Valleys, which represent 60%-70% of the total wheat production in China, the large-scale genotyping of wheat germplasms has not yet been performed in terms of vernalization and photoperiod response alleles, limiting the use of Chinese wheat germplasms to a certain extent.ResultsIn this study, 173 winter wheat cultivars and 51 spring wheat cultivars from China were used to identify allelic variations of vernalization and photoperiod genes as well as copy number variations of Ppd-B1 and Vrn-A1. Two new co-dominant markers were developed in order to more precisely examine Vrn-A1b, Vrn-B1a, and Vrn-B1b. Two novel alleles at the Vrn-B3 locus were discovered and were designated Vrn-B3b and Vrn-B3c. Vrn-B3b had an 890-bp insertion in the promoter region of the recessive vrn-B3 allele, and Vrn-B3c allele had 2 deletions (a 20-bp deletion and a 4-bp deletion) in the promoter region of the dominant Vrn-B3a allele. Cultivar Hemai 26 lacked the Vrn-A1 gene. RT-PCR indicated that the 890-bp insertion in the Vrn-B3b allele significantly reduced the transcription of the Vrn-B3 gene. Cultivars Chadianhong with the Vrn-B3b allele and Hemai 26 with a Vrn-A1-null allele possessed relatively later heading and flowering times compared to those of Yanzhan 4110, which harbored recessive vrn-B3 and vrn-A1 alleles. Through identification of photoperiod genes, 2 new polymorphism combinations were found in 6 winter wheat cultivars and were designated Hapl-VII and Hapl-VIII, respectively. Distribution of the vernalization and photoperiod genes indicated that all recessive alleles at the 4 vernalization response loci, truncated “Chinese Spring” Ppd-B1 allele at Ppd-B1 locus and Hapl-I at the Ppd-D1 locus were predominant in Chinese winter wheat cultivars.ConclusionThis study illustrated the distribution of vernalization and photoperiod genes and identified 2 new Vrn-B3 alleles, 1 Vrn-A1-null allele, and two new Ppd-D1 polymorphism combinations, using developed functional markers. Results of this study have the potential to provide useful information for screening relatively superior wheat cultivars for better adaptability and maturity.

Mapping QTLs Controlling Agronomic Traits in the ‘Attila’ × ‘CDC Go’ Spring Wheat Population under Organic Management using 90K SNP Array

“…between 293 and 300 cM on chromosome 5A (Table 2). In bread wheat, the three vernalization response genes (Vrn-1, Vrn-2, and Vrn-3) directly influence both flowering and maturity (Galiba et al, 1995;Dubcovsky et al, 1998;Iwaki et al, 2002), of which Vrn-A1 mapped to the long arm of chromosome 5A (Preston and Kellogg, 2008;Chen et al, 2013). In bread wheat, the three vernalization response genes (Vrn-1, Vrn-2, and Vrn-3) directly influence both flowering and maturity (Galiba et al, 1995;Dubcovsky et al, 1998;Iwaki et al, 2002), of which Vrn-A1 mapped to the long arm of chromosome 5A (Preston and Kellogg, 2008;Chen et al, 2013).…”

“…Samples of DNA were genotyped at the University of Saskatchewan Wheat Genomics laboratory in Saskatoon, Canada, with the 90K Illumina iSelect SNP array that consisted of 81,587 SNPs (Wang et al, 2014). We also screened the two parents for polymorphism for photoperiod response (Ppd-B1 and Ppd-D1) (Beales et al, 2007), vernalization response (Vrn-A1 and Vrn-B1) (Chen et al, 2013), and height-reducing Rht-B1 (Ellis et al, 2002) genespecific markers at the Agricultural Genomics and Proteomics tillers, required 53 d to flowering and 90 d to maturity, was 70 cm tall, produced 3.1 Mg ha −1 grain yield, and had 13% grain protein content (Supplemental Material 1). Additional filtering was then done, as described in one of our previous studies by Perez-Lara et al (2016), to select only SNPs that segregated in a biallelic pattern based on data from multiple mapping populations available to our programs.…”

Analysis of the VERNALIZATION-A1 exon-4 polymorphism in polyploid wheat

“…В неко- торых исследованиях гаплотип экзона-4 выявляли в ходе анализа хроматограмм секвенирования соответствующих ампликонов (Zhang et al, 2015) или субклонов (Chen et al, 2013), а также с использованием KASP-генотипирования (Díaz et al, 2012). В отличие от предложенных в насто-ящем исследовании способов, они более трудоемкие, экономически затратные и требуют больше времени для получения результата, поскольку содержат большее число этапов анализа.…”

Distribution of the Vrn-D1b allele associated with facultative growth habit in Chinese wheat accessions

“…As Vrn-D1b has the same deletion in the first intron as Vrn-D1a at the Vrn-D1 locus, cultivars with the dominant Vrn-D1 allele identified in previous studies Euphytica Sun et al 2009;Zhang et al 2009;Jiang et al 2010;Zhang et al 2010;Zhao et al 2010;Chen et al 2013;Sun et al 2013) by a molecular marker designed to detect the deletion, included those with either Vrn-D1a or Vrn-D1b. They were specifically selected for this study to distinguish between the two genotypes.…”

“…YHRR is the largest wheat zone, accounting for 60-70 % of the total wheat acreage in China (Jin 1996). Previous studies indicated that the dominant Vrn-D1 allele was the most widely distributed in Chinese wheat cultivars Sun et al 2009;Zhang et al 2009;Jiang et al 2010;Zhang et al 2010;Zhao et al 2010;Chen et al 2013;Sun et al 2013). However, the origin and distribution of the novel Vrn-D1b allele was not clear.…”