Genomic characterization of the Hordeum vulgare DEP1 (HvDEP1) gene and its diversity in a collection of barley accessions
Genomic characterization of the Hordeum vulgare DEP1 (HvDEP1) gene and its diversity in a collection of barley accessions
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DOI：
10.1007/s10681-014-1089-1
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发表时间：
2014-07-01
期刊：
影响因子：
1.9
通讯作者：
Belzile, Francois
中科院分区：
文献类型：
--
作者：
Belanger, Sebastien;Gauthier, Melanie;Belzile, Francois
谷物产量潜力由三个主要组成部分的贡献决定：单株花序数、每花序粒数和平均粒重。在水稻中，紧密直立穗（DEP 1）基因影响花序的三个重要数量性状，并且在大麦和小麦中已经报道了DEP 1同源物。在这项工作中，我们已经进行了详细的表征大麦DEP 1（HvDEP 1）基因。我们获得了其转录物的全长序列，研究了其在各种组织中的表达，将其遗传映射到染色体5 H，并测量了其在加拿大大麦品种中的核苷酸多样性。该基因有一个特别长的5'非翻译区（297 bp），含有一个上游开放阅读框（uORF），编码70个氨基酸的预测肽。在我们检查的所有六种草中发现了含有推定的uORF的类似长的5' UTR。虽然HvDEP 1转录本可以检测到在所有的组织测试，它是最高的分生组织。在167个大麦品种的集合中，观察到低水平的多态性（pi = 0.001），并且检测到37个SNPs/indels，其中没有一个导致HvDEP 1蛋白的氨基酸序列的变化，定义了8个单倍型。在83个六行类型中，多样性特别低，除了一个之外，所有类型都具有完全相同的单倍型。我们认为，HvDEP 1参与细胞生长和分化的控制，保守的uORF可能在其转录后调控中发挥作用，并且该基因在两排和六排加拿大精英种质中经历了非常不同的选择历史。
Grain yield potential in cereals results from the contributions of three main components: inflorescence number per plant, grain number per inflorescence and mean grain weight. In rice, the Dense and erect panicle (DEP1) gene affects three important quantitative traits of the inflorescence and DEP1 homologs have been reported in barley and wheat. In this work, we have performed a detailed characterization of the barley DEP1 (HvDEP1) gene. We obtained a full-length sequence of its transcript, examined its expression in various tissues, genetically mapped it to chromosome 5H and measured its nucleotide diversity in a collection of barley cultivars from Canada. This gene has an exceptionally long 5' UTR (297 bp) that contains an upstream open reading frame (uORF) coding for a predicted peptide of 70 amino acids. A similarly long 5' UTR containing a putative uORF was found in all six grass species that we examined. Although HvDEP1 transcripts could be detected in all tissues tested, it was highest in meristematic tissues. In a collection of 167 barley cultivars, a low level of polymorphism was observed (pi = 0.001) and the 37 SNPs/indels detected, none of which result in changes in the amino acid sequence of the HvDEP1 protein, defined 8 haplotypes. Diversity was especially low among 83 six-row types, all but one of which carried the exact same haplotype. We suggest that HvDEP1 is involved in the control of cellular growth and differentiation, that the conserved uORF may play a role in its post-transcriptional regulation and that this gene has undergone a very different history of selection within the two-row and six-row Canadian elite germplasm.