RNA-Seq analysis and development of SSR and KASP markers in lentil (Lens culinaris Medikus subsp. culinaris)
文献类型： 外文期刊
作者： Wang, Dong 1 ; Yang, Tao 2 ; Liu, Rong 2 ; Li, Nana 1 ; Wang, Xiaomu 1 ; Sarker, Ashutosh 4 ; Zhang, Xiaodong 1 ; Li, Run 1 ;
作者机构： 1.Minist Agr, Shandong Prov Key Lab Crop Genet Improvement Ecol, Shandong Ctr Crop Germplasm Resources, Shandong Res Stn Crop Gene Resource & Germplasm E, Jinan 250100, Shandong, Peoples R China
2.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100081, Peoples R China
3.Shandong Normal Univ, Coll Life Sci, Jinan 250014, Shandong, Peoples R China
4.Int Ctr Agr Res Dry Areas ICARDA, New Delhi 110012, India
关键词： Lentil; RNA-Seq; EST-SSR; KASP; Genetic diversity
期刊名称：CROP JOURNAL （ 影响因子：4.407； 五年影响因子：5.687 ）
ISSN： 2095-5421
年卷期： 2020 年 8 卷 6 期
页码：
收录情况： SCI
摘要： Lentil (Lens culinaris Medikus subsp. culinaris, 2n = 14) is a cool-season legume with high production potential for multiple uses. However, limited molecular research has been conducted in this species owing to its large genome, which impedes the generation of genome sequences and the development of molecular markers. In this study, more than 1.37 billion filtered clean reads were collected by RNA-Seq of six diverse lentil accessions and 217,836 transcripts and 161,095 unigenes were de novo assembled, yielding respectively 257.1 and 240.6 million nucleotides. The mean transcript length was 1180 bp and the N50 and N90 lengths were respectively 2075 and 479 bp. The mean length of the unigenes was 1494 by and their N50 and N90 values were respectively 2203 and 714 bp. The unigenes were annotated against seven databases. The FLOWERING LOCUS T (FT) gene homolog in lentil showed high protein sequence similarity to the FT gene homologs of pea and alfalfa. On the basis of the RNA-Seq analysis, 26,449 EST-SSR markers were designed in silico, and 276 preliminarily screened markers were selected to evaluate polymorphism in 94 diverse lentil accessions. In total, 125 (4529%) of 276 EST-SSR markers were found to be polymorphic. A total of 130,073 SNP loci were detected and 78 (61.41%) of 127 SNPs were successfully converted to KASP markers. Population genetic analyses of the lentil accessions with EST-SSR and KASP markers revealed similar genetic structures, suggesting that the RNA-Seq-generated resources and the developed markers are reliable for use in molecular marker-assisted breeding of lentil. (C) 2020 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.
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