成都生物所在Plos one分析西藏青稞籽粒发育转录组
青稞(Hordewn vulgare L. var. nudum Hook, f. 2N=14)，即裸大麦，属于禾本科小麦族大麦属，是大麦的变种之一，因其在成熟时颖果易与稃分离而得名。青藏高原藏区人民把裸大麦叫做青稞。青稞是青藏高原藏区的主要农作物，是重要的口粮，也是重要的食品加工原料及牲畜饲料。研究表明青稞富含 β-葡聚糖、膳食纤维、矿物质等营养成分，具有很高的保健价值。近年来优质青稞选育与应用受到广泛的关注，而青稞籽粒发育中品质性状形成的分子机理研究对改良青稞品质极其重要。
中国科学院成都生物研究所余懋群研究员课题组陈欣博士等利用第二代高通量测序技术(Illumina HiSeq™ 2000)，对品质性状具差异的两青稞材料不同发育时期的籽粒进行转录组分析，分别获得13,069,860和12,918,520条clean reads，对两品种进行De nove组装共获得48,863 和45,788个unigene，其平均长度分别为549 bp与498 bp。将两个unigene基因集进一步组装，获得46,485个非冗余的“All-Unigene”，总长度为25,192,406 bp，平均长度为542 bp。
通过对All-Unigene NR、Swiss-Prot、COG及KEGG注释的进一步分析，鉴定出373个品质相关的unigene，包含淀粉代谢途径的基因、贮藏蛋白编码基因、必需氨基酸代谢途径基因和种子成熟相关基因。分析了淀粉、β-葡聚糖以及蛋白合成途径相关基因表达模式，推测了候选的关键基因;并且根据获得的EST数据鉴定了大量EST-SSR位点和EST-SNP多态性位点。该研究为进一步研究种子发育和品质相关基因奠定了重要的基础。
该研究结果发表于PLoS ONE。
原文摘要：
Xin Chen, Hai Long, Ping Gao, Guangbing Deng, Zhifen Pan, Junjun Liang, Yawei Tang, Nyima Tashi, Maoqun Yu
Background
Hulless barley is attracting increasing attention due to its unique nutritional value and potential health benefits. However, the molecular biology of the barley grain development and nutrient storage are not well understood. Furthermore, the genetic potential of hulless barley has not been fully tapped for breeding.
Methodology/Principal Findings
In the present study, we investigated the transcriptome features during hulless barley grain development. Using Illumina paired-end RNA-Sequencing, we generated two data sets of the developing grain transcriptomes from two hulless barley landraces. A total of 13.1 and 12.9 million paired-end reads with lengths of 90 bp were generated from the two varieties and were assembled to 48,863 and 45,788 unigenes, respectively. A combined dataset of 46,485 All-Unigenes were generated from two transcriptomes with an average length of 542 bp, and 36,278 among were annotated with gene descriptions, conserved protein domains or gene ontology terms. Furthermore, sequences and expression levels of genes related to the biosynthesis of storage reserve compounds (starch, protein, and β-glucan) were analyzed, and their temporal and spatial patterns were deduced from the transcriptome data of cultivated barley Morex.
Conclusions/Significance
We established a sequences and functional annotation integrated database and examined the expression profiles of the developing grains of Tibetan hulless barley. The characterization of genes encoding storage proteins and enzymes of starch synthesis and (1–3;1–4)-β-D-glucan synthesis provided an overview of changes in gene expression associated with grain nutrition and health properties. Furthermore, the characterization of these genes provides a gene reservoir, which helps in quality improvement of hulless barley.
作者：成都生物所
