Huang L K, Yan H D, Zhao X X, Zhang X Q, Wang J, Frazier T, Yin G, Huang X, Yan D F, Zang W J, Ma X, Peng Y, Yan Y H, Liu W
Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
Agronomy Department, University of Florida, Gainesville, FL, 32611, USA.
Mol Ecol Resour. 2015 Nov;15(6):1497-509. doi: 10.1111/1755-0998.12418. Epub 2015 May 7.
Orchardgrass (Dactylis glomerata L.) is a long-lived, cool-season forage grass that is commonly used for hay production. Despite its economic importance, orchardgrass genome remains relatively unexplored. In this study, we used Illumina RNA sequencing to identify gene-associated molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), as well as heat stress-induced differentially expressed genes (DEGs) in two orchardgrass genotypes, 'Baoxing' (heat resistant) and '01998' (heat susceptible). Approximately 163 million high-quality trimmed reads were generated from 207 million raw reads using the Illumina HiSeq 2000 platform. A total of 126,846 unigenes were obtained after de novo assembly of the trimmed reads, and 40,078 unigenes were identified as coding sequences (CDSs). Based on the assembled unigenes, 669,300 high-quality SNPs, including 416,099 transitions and 257,736 transversions, were contained in 75,875 unigenes. In addition, a total of 8475 microsatellites were detected in 7764 unigenes. When placed under heat stress, the total number of DEGs in 'Baoxing' (3527) was higher than in '01998' (2649), indicating that in comparison with heat-susceptible '01998', heat-resistant 'Baoxing' seems to have more unigenes that respond to heat stress. The high-throughput transcriptome sequencing of orchardgrass under heat stress provides useful information for gene identification and for the development of SNP and SSR molecular markers. The comparison of DEGs under different periods of heat stress allowed us to identify a wealth of candidate DEGs that can be further analysed in order to determine the genetic mechanisms underlying heat tolerance in orchardgrass.
鸭茅（Dactylis glomerata L.）是一种多年生的冷季型饲草，常用于干草生产。尽管其具有经济重要性，但鸭茅基因组仍相对未被充分研究。在本研究中，我们使用Illumina RNA测序来鉴定与基因相关的分子标记，包括简单序列重复（SSR）和单核苷酸多态性（SNP），以及在两个鸭茅基因型‘宝兴’（耐热）和‘01998’（热敏感）中热胁迫诱导的差异表达基因（DEG）。使用Illumina HiSeq 2000平台从2.07亿条原始 reads 中生成了约1.63亿条高质量的修剪后 reads。对修剪后的 reads 进行从头组装后，共获得126,846个单基因，其中40,078个单基因被鉴定为编码序列（CDS）。基于组装的单基因，75,875个单基因中包含669,300个高质量SNP，其中包括416,099个转换和257,736个颠换。此外，在7764个单基因中总共检测到8475个微卫星。在热胁迫下，‘宝兴’（3527个）中的DEG总数高于‘01998’（2649个），这表明与热敏感的‘01998’相比，耐热的‘宝兴’似乎有更多响应热胁迫的单基因。热胁迫下鸭茅的高通量转录组测序为基因鉴定以及SNP和SSR分子标记的开发提供了有用信息。对不同热胁迫时期的DEG进行比较，使我们能够鉴定出大量候选DEG，可对其进行进一步分析以确定鸭茅耐热性的遗传机制。
