Identification and distribution of VERNALIZATION1 alleles in Chinese barley (Hordeum vulgare) germplasm

Abstract

VERNALIZATION1 (VRN1) is a central regulator of the vernalization requirement, which affects the yield and geographical distribution of Triticeae crops through regulation of the flowering time. The first intron (Intron I) of VRN1 contains putative cis-elements that mediate repression of VRN1 expression. Allelic variations in Intron I are closely associated with increased VRN1 expression in vernalization-responsive accessions in the absence of vernalization. In this study, diagnostic molecular markers were developed to distinguish the main 12 known alleles, including a new allele, of barley (Hordeum vulgare) VRN1 (HvVRN1), and to investigate HvVRN1 alleles in 373 barley varieties from major agroecological regions in China. The new allele, HvVRN1-11, with a 3172-bp deletion in Intron I of HvVRN1, was identified in a Chinese barley landrace. Analysis of eight polymorphic sites flanking major variations in Intron I of HvVRN1 classified the 12 HvVRN1 alleles into five distinct groups. Compared with modern commercial barley, landraces possessed greater genetic diversity and contained the majority of HvVRN1 alleles, especially in the winter barley regions. HvVRN1 diversity in terms of allele number reduced significantly (P \ 0.01) along with higher growing latitudes, but increased in accessions carrying the winter HvVRN2 allele. Wild-type HvVRN1 and the HvVRN1-8 allele showed the most widespread distribution in most regions whereas HvVRN1-1 & HvVRN1-8, and HvVRN1-5 are predominant in the Inner Mongolian Plateau spring barley region and the Northeast Plain spring barley region, respectively, with relatively higher latitudes. Compared with landraces, the frequency of HvVRN1-8 decreased while wild-type HvVRN1 increased significantly (P \ 0.01) in commercial varieties. Our study classified HvVRN1 genetic diversity in a large collection of Chinese germplasm and provided a tool for identifying HvVRN1 alleles in barley breeding populations.

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

“…Mutations in VRN-H1 and the loss of strong cold requirements allowed the expansion of cultivated barley to areas where spring types are more suitable (von Bothmer et al 2003 ; Cockram et al 2011 ), although this explanation can be extended to encompass the role of less strict winter types, adapted to fall sowings in areas with warm winters. In fact, several studies have reported ample allelic variation at VRN-H1 and its relation with geographical distribution, in accordance with this hypothesis (Cockram et al 2007a , b ; Saisho et al 2011 ; Zhang et al 2015a , b ; Dondup et al 2016 ; Contreras‐Moreira et al 2019 ). Besides vernalization response, the VRN-H1 region has also been associated with winter survival in the field and frost tolerance (Francia et al 2004 ; Cuesta-Marcos et al 2015 ), with deep implications on the geographical distribution of barley cultivars.…”

“…Polymorphisms at this gene are richer in wheat than in barley. Besides deletions in the first intron (Fu et al 2005 ), like in barley, many mutations have been described in other regulatory regions and coding sequence, all associated with increased expression of the gene and accelerated flowering in the absence of vernalization (Yan et al 2003 , 2004a ; Chu et al 2011 ; Li et al 2013 ; Muterko et al 2015 ; Zhang et al 2015a , b ; Kippes et al 2018 ). These mutations give rise to spring dominant alleles, with the VRN-A1 allele showing the strongest effect on flowering time (lack of vernalization requirement), and VRN-B1 and VRN-D1 alleles showing a weaker effect (reduced vernalization requirement) (Trevaskis et al 2003 ).…”

“…The molecular mechanisms underlying photoperiod sensitivity may differ between the two species. Allelic diversity in PPD-1 results from deletions or a transposon insertion in the promoter, and from copy number variation ( PPD-B1 ) (Wilhelm et al 2009 ; Bentley et al 2011 ; Díaz et al 2012 ; Bentley et al 2013 ; Nishida et al 2013b ; Zhang et al 2015a , b ; Würschum et al 2019 ). The homeologue in D subgenome is the major factor affecting flowering time in hexaploid wheat germplasm (Kiss et al 2014 ; Langer et al 2014 ; Würschum et al 2018 ).…”

A multiplex PCR marker distinguishes between a series of four LanFTc1 alleles regulating flowering time in narrow‐leafed lupin (Lupinus angustifolius)

“…This was well demonstrated in the presented case study, where unexpected hybrids derived from natural cross pollination events were identified during the 2020 F 4 field trial (Table S3). This MADS-box transcription factor gene, where 10 deletions (0.5 to 8.9 Kb in size) and one insertion (0.7 Kb) facilitate varying degrees of VRN-H1 de-repression and phenological variation in the absence of vernalization (Cockram et al, 2007(Cockram et al, , 2011Fu et al, 2005;Hemming et al, 2009;Szűcs et al, 2007;von Zitzewitz et al, 2005;Zhang et al, 2015). Similarly, two well-documented hotspots within the 14 Kb coding sequence of the DMD gene are heavily concentrated in large INDELs spanning one or more exons that account for approximately two thirds of all reported human DMD diseases (Aartsma-Rus et al, 2016;Iskandar et al, 2019).…”

“…Similarly, two well-documented hotspots within the 14 Kb coding sequence of the DMD gene are heavily concentrated in large INDELs spanning one or more exons that account for approximately two thirds of all reported human DMD diseases (Aartsma-Rus et al, 2016;Iskandar et al, 2019). In both cases, the original multiplex PCR assays designed to genotype these hotspots have been frequently revised over the years to accommodate new INDELs as they have been discovered (Abbs et al, 1991;Beggs et al, 1990Beggs et al, , 1991Chamberlain et al, 1988Chamberlain et al, , 1990Cockram et al, 2009;Kunkel et al, 1991;Stockley et al, 2006;Zhang et al, 2015). The LanFTc1 multiplex PCR assay could likewise be adapted in future if necessary.…”