Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton
Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton
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DOI：
10.1007/s00438-007-0270-9
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发表时间：
2007-11-01
影响因子：
3.1
通讯作者：
Stelly, David M.
中科院分区：
文献类型：
--
作者：
An, Chuanfu;Saha, Sukumar;Stelly, David M.
棉花DNA标记的生物学意义的知识非常有限。SNP是标记具有生物学重要性的基因的潜在功能标记。植物扩展蛋白是一类直接改变细胞壁机械性质的细胞外蛋白质，能够使细胞生长受到突波驱动，并可能影响棉纤维的长度和质量。在这里，我们报告的表达谱的EXPANSIN转录在纤维伸长和SNP标记的发现，评估SNP的特点，并本地化6 EXPANSIN A基因的染色体。棉纤维寡核苷酸微阵列的转录组分析显示，7 EXPANSIN转录差异表达时，有平行极性伸长在纤维发育的早期形态发生，表明主要和次要异构体执行离散的功能在极性伸长和横向扩展。通过系统发育分组和与当代AD基因组棉花的现存A和D基因组亲属的比较，揭示了6个EXPANSIN A基因的祖先和同源进化关系。在所选基因型中，每个核苷酸的平均SNP率为2.35%（每43 bp一个SNP），其中编码区和非编码区的SNP率分别为1.74%和3.99%。在四倍体棉花的亚基因组水平上，EXPANSIN A基因的进化速率不等。通过基因特异性SNP标记建立了6个扩展蛋白A基因中每一个的染色体位置。结果揭示了在棉花等多倍体物种中发现SNP标记的策略。这些标记可用于将候选基因与MAS中的复杂纤维性状相关联。
The knowledge of biological significance associated with DNA markers is very limited in cotton. SNPs are potential functional marker to tag genes of biological importance. Plant expansins are a group of extracellular proteins that directly modify the mechanical properties of cell walls, enable turgor-driven cell extension, and likely affect length and quality of cotton fibers. Here, we report the expression profiles of EXPANSIN transcripts during fiber elongation and the discovery of SNP markers, assess the SNP characteristics, and localize six EXPANSIN A genes to chromosomes. Transcriptome profiling of cotton fiber oligonucleotide microarrays revealed that seven EXPANSIN transcripts were differentially expressed when there was parallel polar elongation during morphogenesis at early stage of fiber development, suggesting that major and minor isoforms perform discrete functions during polar elongation and lateral expansion. Ancestral and homoeologous relationships of the six EXPANSIN A genes were revealed by phylogenetic grouping and comparison to extant A- and D-genome relatives of contemporary AD-genome cottons. The average rate of SNP per nucleotide was 2.35% (one SNP per 43 bp), with 1.74 and 3.99% occurring in coding and noncoding regions, respectively, in the selected genotypes. An unequal evolutionary rate of the EXPANSIN A genes at the subgenome level of tetraploid cotton was recorded. Chromosomal locations for each of the six EXPANSIN A genes were established by gene-specific SNP markers. Results revealed a strategy for discovering SNP markers in a polyploidy species like cotton. These markers could be useful to associate candidate genes with the complex fiber traits in MAS.