National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology (DBT), Government of India, C-127 Industrial Area Phase 8, Mohali 160 071, Punjab, India.
BMC Genomics. 2014 Jan 16;15:29. doi: 10.1186/1471-2164-15-29.
The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments.
Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions.
The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers.
栽培小麦（Triticum aestivum L.）具有独特的面粉品质，可以加工成许多终端用途的食品，如面包、意大利面、恰巴提（无酵扁平面饼）、饼干等。目前的小麦品种需要改进加工品质，以满足对更好质量食品的需求不断增长。然而，加工品质非常复杂，受许多基因控制，这些基因尚未被完全探索。为了鉴定由于加工品质和相互作用（品质 x 发育）的变化而导致表达发生变化的候选基因，在两个用于恰巴提品质的不同印度小麦品种组中进行了全基因组转录组研究。了解其表达的时空分布对于设计组织和生长特异性的功能基因组学实验也很重要。
对两个用于恰巴提品质的不同印度小麦品种组在三个种子发育阶段的约 55 K 个转录物的基因特异性双向方差分析，鉴定出 236 个差异表达探针集（10 倍）。在 236 个中，鉴定出 110 个探针集与恰巴提品质有关。许多与加工品质相关的关键基因，如谷蛋白和醇溶蛋白、puroindolines、谷物柔软蛋白、α 和 β 淀粉酶、蛋白酶等，以及许多与细胞和分子功能相关的其他候选基因，都被鉴定出来。方差分析表明，110 个探针集中的 56 个与相互作用（品质 x 发育）有关。大多数探针集在种子发育的早期阶段即时间表达上表现出差异表达。荟萃分析表明，大多数基因在一个或几个生长阶段表达，表明其表达的空间分布。几个候选基因，如前-α/β-醇溶蛋白和γ-醇溶蛋白的差异表达通过 RT-PCR 得到验证。因此，本研究鉴定了一些与品质相关的关键基因，包括许多其他基因、它们的相互作用（品质 x 发育）以及时空分布。
鉴定出的与加工品质有关的候选基因及其表达的时空分布信息，对于通过改变其表达或开发单核苷酸多态性（SNP）标记来设计加工品质改良计划将非常有用。
