Rai Krishan M, Thu Sandi W, Balasubramanian Vimal K, Cobos Christopher J, Disasa Tesfaye, Mendu Venugopal
Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech University Lubbock, TX, USA.
Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA; National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural ResearchAddis Ababa, Ethiopia.
Front Plant Sci. 2016 Aug 31;7:1287. doi: 10.3389/fpls.2016.01287. eCollection 2016.
Biomass based alternative fuels offer a solution to the world's ever-increasing energy demand. With the ability to produce high biomass in marginal lands with low inputs, sorghum has a great potential to meet second-generation biofuel needs. Despite the sorghum crop importance in biofuel and fodder industry, there is no comprehensive information available on the cell wall related genes and gene families (biosynthetic and modification). It is important to identify the cell wall related genes to understand the cell wall biosynthetic process as well as to facilitate biomass manipulation. Genome-wide analysis using gene family specific Hidden Markov Model of conserved domains identified 520 genes distributed among 20 gene families related to biosynthesis/modification of various cell wall polymers such as cellulose, hemicellulose, pectin, and lignin. Chromosomal localization analysis of these genes revealed that about 65% of cell wall related genes were confined to four chromosomes (Chr. 1-4). Further, 56 tandem duplication events involving 169 genes were identified in these gene families which could be associated with expansion of genes within families in sorghum. Additionally, we also identified 137 Simple Sequence Repeats related to 112 genes and target sites for 10 miRNAs in some important families such as cellulose synthase, cellulose synthase-like, and laccases, etc. To gain further insight into potential functional roles, expression analysis of these gene families was performed using publically available data sets in various tissues and under abiotic stress conditions. Expression analysis showed tissue specificity as well as differential expression under abiotic stress conditions. Overall, our study provides a comprehensive information on cell wall related genes families in sorghum which offers a valuable resource to develop strategies for altering biomass composition by plant breeding and genetic engineering approaches.
基于生物质的替代燃料为满足全球不断增长的能源需求提供了一种解决方案。高粱能够在投入较低的边际土地上高产生物质，因此在满足第二代生物燃料需求方面具有巨大潜力。尽管高粱作物在生物燃料和饲料工业中具有重要地位，但目前尚无关于细胞壁相关基因和基因家族（生物合成和修饰）的全面信息。识别细胞壁相关基因对于理解细胞壁生物合成过程以及促进生物质调控至关重要。利用保守结构域的基因家族特异性隐马尔可夫模型进行全基因组分析，鉴定出520个基因，分布在20个与各种细胞壁聚合物（如纤维素、半纤维素、果胶和木质素）生物合成/修饰相关的基因家族中。对这些基因的染色体定位分析表明，约65%的细胞壁相关基因集中在四条染色体（第1 - 4号染色体）上。此外，在这些基因家族中鉴定出56个涉及169个基因的串联重复事件，这可能与高粱基因家族内的基因扩增有关。此外，我们还在一些重要家族（如纤维素合酶、类纤维素合酶和漆酶等）中鉴定出与112个基因相关的137个简单序列重复以及10个miRNA的靶位点。为了进一步深入了解潜在的功能作用，利用公开数据集对这些基因家族在各种组织和非生物胁迫条件下进行了表达分析。表达分析显示了组织特异性以及在非生物胁迫条件下的差异表达。总体而言，我们的研究提供了关于高粱细胞壁相关基因家族的全面信息，为通过植物育种和基因工程方法改变生物质组成的策略开发提供了宝贵资源。
