Development and validation of novel fiber relevant dbEST-SSR markers and their utility in revealing genetic diversity in diploid cotton (Gossypium herbaceum and G. arboreum)
Development and validation of novel fiber relevant dbEST-SSR markers and their utility in revealing genetic diversity in diploid cotton (Gossypium herbaceum and G. arboreum)
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DOI：
10.1016/j.indcrop.2015.12.061
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发表时间：
2016-05-01
影响因子：
5.9
通讯作者：
Parihar, Akarsh
中科院分区：
文献类型：
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作者：
Parekh, Mithil J.;Kumar, Sushil;Parihar, Akarsh
与四倍体棉花相比，二倍体棉花尤其是草棉在包括分子标记在内的基因组资源方面比较贫乏。公共数据库中的表达序列标签（EST）是宝贵的资源，为鉴定简单重复序列（SSR）标记提供了机会。利用棉花ESTs数据库开发新的EST-SSR标记。对1，31，464条dbEST（G. hirsutum、92，570和G. arboreum，38，894）导致28，718个单基因（17，019个单基因和11，699个重叠群）具有1，760个SSR。平均每16.3kb的单基因含有1个SSR标记。AG类在二核苷酸基序中最常见（45%），而AAG类（25%）在三核苷酸基序中占主导地位。从棉花纤维细胞和胚珠的EST序列中筛选出378对新引物。选择了一组与纤维发育相关的60个引物，并在23个G的面板上进行了验证。herbaceum和9个G.树木园基因型。在60个引物中，44个引物共扩增出71个位点，其中多态性位点54个，占76%。多态信息含量（PIC）在0.11 ~ 0.74之间。II类重复SSR基序比I类重复SSR标记更具多态性。所有基因型组合间的Nei’s相异系数在0.02 ~ 0.49之间，平均值为0.24。UPGMA聚类结果以0.23为界值，将32个基因型分为2类。本研究开发的EST-SSR标记将为棉花种质资源鉴定、群体结构分析和QTL定位提供最佳的材料。(C)2015 Elsevier B. V.版权所有。
Compared to tetraploid, diploid cotton especially Gossypium herbaceum are poor in genomic resources including molecular markers. Expressed sequence tags (ESTs) in public databases are valuable resources and offer opportunity for identification of simple sequence repeat (SSR) markers. ESTs data base of cotton were employed for the development of novel EST-SSR markers. Sequence assembly and clustering of 1,31,464 dbESTs (G. hirsutum, 92,570 and G. arboreum, 38,894) resulted in 28,718 unigenes (17,019 singletons and 11,699 contigs) having 1,760 SSRs. On an average, the unigenes contained 1 SSR/16.3 kb of unigene. The AG class was the most common among the dinucleotide motifs (45%), whereas the AAG class (25%) was predominant among the trinucleotide motif. A total of 378 novel primers pairs were developed from the ESTs of cotton fiber cells and ovules. A set of 60 primers associated with fiber development were selected and validated on a panel of 23 G. herbaceum and nine G. arboreum genotypes. Among 60, 44 primers d amplified 71 loci; of which 54 (76%) were polymorphic. The polymorphic information content (PIC) ranged from 0.11-0.74. The class II repeat SSR motifs were more polymorphic than class I repeat SSR markers. Nei's dissimilarity coefficients based on SSR markers among the all pair-wise combinations of genotypes ranged from 0.02 to 0.49 with a mean of 0.24. The UPGMA clustering grouped 32 genotypes in 2 clusters at cut off value of 0.23. The EST-SSR markers developed in our study would be best assets for characterization of germplasm, population structure analysis and QTL mapping in diploid cotton. (C) 2015 Elsevier B.V. All rights reserved.