Allelic variation of row type gene Vrs1 in barley and implication of the functional divergence

Sugiyama, Daisuke; Pourkheirandish, Mohammad; Kanamori, Hajime; Matsumoto, Takashi; Komatsuda, Takao

doi:10.1270/jsbbs.59.621

Cited by 32 publications

(30 citation statements)

References 15 publications

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“…To infer the origin of the deficiens allele (Vrs1.t1), we reanalyzed the sequence of the Vrs1 region (2,062 bp length) from 321 domesticated barley and 136 wild barley accessions (Saisho et al, 2009). Haplotype network analysis revealed that the Vrs1.t1 allele (haplotype 10) was derived from the Vrs1.b2 allele (haplotype 6) through a single nucleotide substitution in exon 3, which resulted in the S184G amino acid substitution, implying that Vrs1.b2 was the immediate ancestral allele of Vrs1.t1 (Fig.…”

Section: The Origin Of Deficiens Barleymentioning

confidence: 99%

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Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Sakuma

Lundqvist²,

Kakei

et al. 2017

Plant Physiol.

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Increasing grain yield is an endless challenge for cereal crop breeding. In barley (Hordeum vulgare), grain number is controlled mainly by Six-rowed spike 1 (Vrs1), which encodes a homeodomain leucine zipper class I transcription factor. However, little is known about the genetic basis of grain size. Here, we show that extreme suppression of lateral florets contributes to enlarged grains in deficiens barley. Through a combination of fine-mapping and resequencing of deficiens mutants, we have identified that a single amino acid substitution at a putative phosphorylation site in VRS1 is responsible for the deficiens phenotype. deficiens mutant alleles confer an increase in grain size, a reduction in plant height, and a significant increase in thousand grain weight in contemporary cultivated germplasm. Haplotype analysis revealed that barley carrying the deficiens allele (Vrs1.t1) originated from two-rowed types carrying the Vrs1.b2 allele, predominantly found in germplasm from northern Africa. In situ hybridization of histone H4, a marker for cell cycle or proliferation, showed weaker expression in the lateral spikelets compared with central spikelets in deficiens. Transcriptome analysis revealed that a number of histone superfamily genes were up-regulated in the deficiens mutant, suggesting that enhanced cell proliferation in the central spikelet may contribute to larger grains. Our data suggest that grain yield can be improved by suppressing the development of specific organs that are not positively involved in sink/source relationships.

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Section: The Origin Of Deficiens Barleymentioning

confidence: 99%

“…A haplotype analysis was performed based on resequencing data of the Vrs1 locus (2,062 bp) from 321 domesticated barley accessions and 136 wild barley accessions (Supplemental Table S8; Saisho et al, 2009). Sequence alignments were performed with ClustalW using MEGA7 software (Kumar et al, 2016).…”

Section: Haplotype Analysismentioning

confidence: 99%

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Sakuma

Lundqvist²,

Kakei

et al. 2017

Plant Physiol.

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“…Previous studies suggested that six-rowed barley evolved from domesticated two-rowed barley through spontaneous mutation (Harlan 1968;Zohary and Hopf 2000;Komatsuda et al 2007). Recently, the function of vrs1 has been further clarified, the wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain leucine zipper I sequence (HvHox1) (Komatsuda et al 2007;Saisho et al 2009). Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes (Komatsuda et al 2007;Saisho et al 2009;Youssef et al 2012).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, the function of vrs1 has been further clarified, the wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain leucine zipper I sequence (HvHox1) (Komatsuda et al 2007;Saisho et al 2009). Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes (Komatsuda et al 2007;Saisho et al 2009;Youssef et al 2012). Loss of function of Vrs1 allele resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype (Komatsuda et al 2007;Saisho et al 2009;Youssef et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Population genetics and phylogenetic analysis of thevrs1nucleotide sequence in wild and cultivated barley

Ren

Wang

Sun

et al. 2014

Genome

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Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

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“…spontaneum accession OUH602 (the OU numbers relate to the Barley and Wild Plant Resource Center collection, http://www.rib.okayama-u.ac.jp/barley/index.html), was obtained from the Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan. The SV numbers represent designators within a core collection designed to capture the global diversity of barley (Saisho et al 2009;Nair et al 2010). Grain of the cultivars "Azumamugi" (AZ), "Kanto Nakate Gold" (KNG), and "Golden Promise" (GP) were supplied by the NIAS Gene Bank, Tsukuba, Japan, that of …”

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An Epiallele at cly1 Affects the Expression of Floret Closing (Cleistogamy) in Barley

Wang

Ning

et al. 2014

Genetics

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The swelling of the lodicule is responsible for floret opening in many grass species, allowing for pollen dispersal and crosspollination. In barley, the closed floret habit (cleistogamy) is under the control of cly1, a gene that operates by inhibiting the development of the lodicule. In non-cleistogamous cultivars, cly1 mRNA is degraded by miR172-directed cleavage, allowing the lodicules to swell; however, in cultivars carrying the recessive allele cly1.b, a single-nucleotide substitution destroys the miR172 target site preventing mRNA cleavage. Barley cv. SV235 is cleistogamous; its cly1 coding sequence is identical to that of cly1.b, but its lodicules do develop, although insufficiently to produce a non-cleistogamous flower. In this cultivar, the downregulation of cly1 is unrelated to miR172-directed mRNA degradation, but rather is caused by an epiallele that represses transcription. Allelic relationships between known cly1 alleles were explored by the quantification of lodicule vascularization and an assessment of the response of the spike to the supply of exogenous auxin. The SV235 phenotype can be manipulated by a pre-anthesis application of 2,4-D, a feature that could be of interest in the context of hybrid barley grain production based on cleistogamy.T HE swelling of the lodicule, a structure found in the floret of many grass species and functionally related to the petal in the hermaphroditic angiosperm flower, drives apart the palea and lemma, thereby opening the floret so that it can release its pollen and be readily cross-pollinated (Briggs 1978). In barley, closed flowering (cleistogamous) variants are known. In some of these, the lodicule fails to swell (Kurauchi et al. 1994;Turuspekov et al. 2004;Honda et al. 2005;Wang et al. 2013). The cleistogamy 1 gene (cly1) has been shown to encode an AP2-protein and is a paralog of HvAP2-like in barley and Q in bread wheat (Simons et al. 2006;Nair et al. 2010;Simonov and Pshenichnikova 2012;Ning et al. 2013). In noncleistogamous barleys, cly1 mRNA is cleaved by an miRNA, with the result that the abundance of full-length gene product remains at a low level. Two cleistogamy alleles are known, cly1.b and cly1.c; in both cases, cly1 mRNA is not cleaved by miR172, resulting in the failure of the lodicule to swell. Exceptionally, in cv. SV235, although its cly1 coding sequence is identical to that of cly1.b, its lodicules do swell at anthesis, although insufficiently to force open the floret. Here, we show the genetic and epigenetic basis of the unusual lodicule development seen in cv. SV235. Materials and Methods Plant materialsGrain of the barley cultivars SV002 (OUA008, "Sanalta"), SV223 (OUU059, "Tammi"), SV230 (OUU305, "Badajoy"), SV235 (OUU326, "France 1"), SV237 (OUU329, "Cygne"), SV241 (OUU351, "Plumage"), SV242 (OUU352, "Imperial"), and SV255 (OUU613, "Otello"), along with the Hordeum vulgare subsp. spontaneum accession OUH602 (the OU numbers relate to the Barley and Wild Plant Resource Center collection, http://www.rib.okayama-u.ac.jp/barley/index...

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Allelic variation of row type gene Vrs1 in barley and implication of the functional divergence

Cited by 32 publications

References 15 publications

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Population genetics and phylogenetic analysis of thevrs1nucleotide sequence in wild and cultivated barley

An Epiallele at cly1 Affects the Expression of Floret Closing (Cleistogamy) in Barley

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