Allelic variation at the vernalization and photoperiod sensitivity loci in Chinese winter wheat cultivars (Triticum aestivum L.)

Abstract

A total of 205 wheat cultivars from the Yellow and Huai valley of China were used to identify allelic variations of vernalization and photoperiod response genes, as well as the copy number variations (CNVs) of Ppd-B1 and Vrn-A1 genes. A novel Vrn-D1 allele with 174-bp insertion in the promoter region of the recessive allele vrn-D1 was discovered in three Chinese wheat cultivars and designated as Vrn-D1c. Quantitative real-time polymerase chain reaction showed that cultivars with the Vrn-D1c allele exhibited significantly higher expression of the Vrn-D1 gene than that in cultivars with the recessive allele vrn-D1, indicating that the 174-bp insertion of Vrn-D1c contributed to the increase in Vrn-D1 gene expression and caused early heading and flowering. The five new cis-elements (Box II-like, 3-AF1 binding site, TC-rich repeats, Box-W1 and CAT-box) in the 174-bp insertion possibly promoted the basal activity level of Vrn-D1 gene. Two new polymorphism combinations of photoperiod genes were identified and designated as Ppd-D1_Hapl-IX and Ppd-D1_Hapl-X. Association of the CNV of Ppd-B1 gene with the heading and flowering days showed that the cultivars with Ppd-B1_Hapl-VI demonstrated the earliest heading and flowering times, and those with Ppd-B1_Hapl-IV presented the latest heading and flowering times in three cropping seasons. Distribution of the vernalization and photoperiod response genes indicated that all recessive alleles at the four vernalization response loci, Ppd-B1_Hapl-I at Ppd-B1 locus, and Ppd-D1_Hapl-I at the Ppd-D1 locus were predominant in Chinese winter wheat cultivars. This study can provide useful information for wheat breeding programs to screen wheat cultivars with relatively superior adaptability and maturity.

INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow‐leafed lupin (Lupinus angustifolius L.)

“…The largest and most widely published allelic series identified to date involves VRN‐1 , a MADS‐box transcription factor that is orthologous to APETALA1 in Arabidopsis (Yan et al, ) and that is involved in maintaining down‐regulation of floral repressors following vernalization within members of the Poaceae family (A. Chen & Dubcovsky, ). Within the promoter and intronic regions, a staggering number of INDELs ranging in size from 20 to 6,850 bp, in addition to a single SNP, have been identified in the A, B, D, and G genomes of various diploid, tetraploid, and hexaploid wild and domestic wheats and their progenitors (Fu et al, ; Golovnina, Kondratenko, Blinov, & Goncharov, ; Konopatskaia, Vavilova, Kondratenko, Blinov, & Goncharov, ; Milec, Tomková, Sumíková, & Pánková, ; Muterko, Balashova, Cockram, Kalendar, & Sivolap, ; Santra, Santra, Allan, Campbell, & Kidwell, ; Shcherban, Efremova, & Salina, ; Takumi, Koyamam, Fujiwara, & Kobayashi, ; Yan et al, ; Zhang, Gao, Wang, Chen, & Cui, ), plus the H genome of barley ( Hordeum vulgare L.; Fu et al, ). Our study also adds to others in Arabidopsis (Liu et al, ; Schwartz et al, ), perennial ryegrass ( Lolium perenne ; Skøt et al, ), and wheats and barley (F. Chen et al, ; Yan et al, ) showing that FT orthologues have similarly been a common target for the evolution of natural flowering time variation in a range of plant families.…”

VRN1 genes variability in tetraploid wheat species with a spring growth habit

“…Vrn-B1dic allele is characterized by unexpected high dissimilarity in compare to the vrn-B1 allele. If we exclude the deletions and insertions cases the other dominant alleles of VNR1 genes of di- and polyploidy wheats differ from recessive alleles by several SNPs [19, 22, 23, 27, 29]. Alternatively, we could suggest that the Vrn-B1dic represent the pseudogene copy originated by duplication within one genome.…”

“…Most of the dominant alleles of VRN-B1 and VRN-D1 genes possess deletions in the first intron ( Vrn-B1a , Vrn-B1b , Vrn-B1c and Vrn-D1a ) [16, 19, 22, 24–27]. Several recently identified alleles ( Vrn-B1ins, Vrn-D1c, Vrn-D1s ) are characterized by different insertions within the promoter region [19, 28, 29]. The Vrn - D1b is characterized by the deletion in intron 1 identical to Vrn - D1a allele and a single nucleotide mutation at promoter and is associated with facultative growth habit [30].…”

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.…”

“…Исследование полиморфизма экзона-4 осложняется наличием нескольких копий гена VRN-A1 с различными гаплотипами в разных соотношениях. В предыдущих исследованиях идентификация образцов, несущих одно-временно дикий и мутантный типы четвертого экзона, проводилась по наличию двойного пика на хроматограм-ме секвенирования (Díaz et al, 2012;Zhang et al, 2015). Однако не всегда удается четко отличить такую область хроматограммы от шума, особенно в случаях, где число копий с различными гаплотипами экзона-4 неодинаково.…”