Dataset Information

Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type.

ABSTRACT: The naturally occurring wild barley mutant eibi1/hvabcg31 suffers from severe water loss due to the permeable leaf cuticle. Eibi1/HvABCG31 encodes a full ATP-binding cassette (ABC) transporter, HvABCG31, playing a role in cutin deposition in the elongation zone of growing barley leaves. The eibi1 allele has pleiotropic effects on the appearance of leaves, plant stature, fertility, spike and grain size, and rate of germination. Comparative transcriptome profile of the leaf elongation zone of the eibi1 mutant as well as its isogenic wild type showed that various pathogenesis-related genes were up-regulated in the eibi1 mutant. The known cuticle-related genes that we analyzed did not show significant expression difference between the mutant and wild type. These results suggest that the pleiotropic effects may be a compensatory consequence of the activation of defense genes in the eibi1 mutation. Furthermore, we were able to find the mutation of the eibi1/hvabcg31 allele by comparing transcript sequences, which indicated that the RNA-Seq is useful not only for researches on general molecular mechanism but also for the identification of possible mutant genes.

SUBMITTER: Zhou Q

PROVIDER: S-EPMC5738607 | biostudies-literature | 2017 Oct-Dec

REPOSITORIES: biostudies-literature

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Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type.

Zhou Qin Q Wang Aidong A Duan Ruijun R Yan Jun J Zhao Gang G Nevo Eviatar E Chen Guoxiong G

Genetics and molecular biology 20171023 4

The naturally occurring wild barley mutant eibi1/hvabcg31 suffers from severe water loss due to the permeable leaf cuticle. Eibi1/HvABCG31 encodes a full ATP-binding cassette (ABC) transporter, HvABCG31, playing a role in cutin deposition in the elongation zone of growing barley leaves. The eibi1 allele has pleiotropic effects on the appearance of leaves, plant stature, fertility, spike and grain size, and rate of germination. Comparative transcriptome profile of the leaf elongation zone of the ...[more]

PMID: 29064514

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Project description:BackgroundThe cuticle is an important adaptive structure whose origin played a crucial role in the transition of plants from aqueous to terrestrial conditions. HvABCG31/Eibi1 is an ABCG transporter gene, involved in cuticle formation that was recently identified in wild barley (Hordeum vulgare ssp. spontaneum). To study the genetic variation of HvABCG31 in different habitats, its 2 kb promoter region was sequenced from 112 wild barley accessions collected from five natural populations from southern and northern Israel. The sites included three mesic and two xeric habitats, and differed in annual rainfall, soil type, and soil water capacity.ResultsPhylogenetic analysis of the aligned HvABCG31 promoter sequences clustered the majority of accessions (69 out of 71) from the three northern mesic populations into one cluster, while all 21 accessions from the Dead Sea area, a xeric southern population, and two isolated accessions (one from a xeric population at Mitzpe Ramon and one from the xeric 'African Slope' of "Evolution Canyon") formed the second cluster. The southern arid populations included six haplotypes, but they differed from the consensus sequence at a large number of positions, while the northern mesic populations included 15 haplotypes that were, on average, more similar to the consensus sequence. Most of the haplotypes (20 of 22) were unique to a population. Interestingly, higher genetic variation occurred within populations (54.2%) than among populations (45.8%). Analysis of the promoter region detected a large number of transcription factor binding sites: 121-128 and 121-134 sites in the two southern arid populations, and 123-128,125-128, and 123-125 sites in the three northern mesic populations. Three types of TFBSs were significantly enriched: those related to GA (gibberellin), Dof (DNA binding with one finger), and light.ConclusionsDrought stress and adaptive natural selection may have been important determinants in the observed sequence variation of HvABCG31 promoter. Abiotic stresses may be involved in the HvABCG31 gene transcription regulations, generating more protective cuticles in plants under stresses.

Project description:Wild barley (Hordeum vulgare ssp. spontaneum) has strong grain dormancy, a trait that may enhance its survival in non-cultivated environments; by contrast, cultivated barley (Hordeum vulgare ssp. vulgare) has weaker dormancy, allowing uniform germination in cultivation. Malting barley cultivars have been bred for especially weak dormancy to optimize their use in malt production. Here, we analyzed the genetic mechanism of this difference in seed dormancy, using recombinant inbred lines (RILs) derived from a cross between the wild barley accession 'H602' and the malting barley cultivar 'Kanto Nakate Gold (KNG)'. Grains of H602 and KNG harvested at physiological maturity and dried at 30°C for 7 days had germination of approximately 0 and 100%, respectively. Analysis of quantitative trait loci (QTL) affecting grain dormancy identified the well-known major dormancy QTL SD1 and SD2 (located near the centromeric region and at the distal end of the long arm of chromosome 5H, respectively), and QTL at the end of the long arm of chromosome 4H and in the middle of the long arm of chromosome 5H. We designated these four QTL Qsd1-OK, Qsd2-OK, Qsdw-4H, and Qsdw-5H, and they explained approximately 6, 38, 3, and 13% of the total phenotypic variation, respectively. RILs carrying H602 alleles showed increased dormancy levels for all QTL. The QTL acted additively and did not show epistasis or QTL-environment interactions. Comparison of QTL locations indicated that all QTL except Qsdw-5H are likely the same as the QTL previously detected in the doubled haploid population from a cross between the malting cultivar 'Haruna Nijo' and 'H602.' We further examined Qsd2-OK and Qsdw-5H by analyzing the segregation of phenotypes and genotypes of F2 progenies derived from crosses between RILs carrying specific segments of chromosome 5H from H602 in the KNG background. This analysis confirmed that the two genomic regions corresponding to these QTL are involved in the regulation of grain dormancy. Germination tests of F1 grains derived from reciprocal crosses between H602 and KNG revealed that the H602 strong dormancy phenotype shows maternal inheritance with incomplete dominance. These results provide new insight into the mechanisms regulating grain dormancy in barley.

Dataset Information

Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type.

Publications

Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type.

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