RNA-Seq analysis and development of SSR and KASP markers in lentil (Lens culinaris Medikus subsp. culinaris)
Dong Wang,
Tao Yang,
Rong Liu,
Nana Li,
Xiaomu Wang,
Ashutosh Sarker,
Xiaodong Zhang,
Runfang Li,
Yanyan Pu,
Guan Li,
Yuning Huang,
Yishan Ji,
Zhaojun Li,
Qian Tian,
Xuxiao Zong,
Hanfeng Ding
Affiliations
Dong Wang
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Tao Yang
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Rong Liu
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Nana Li
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China
Xiaomu Wang
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China
Ashutosh Sarker
International Center for Agricultural Research in the Dry Areas (ICARDA), New Delhi 110012, India
Xiaodong Zhang
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China
Runfang Li
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China
Yanyan Pu
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China
Guan Li
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Yuning Huang
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Yishan Ji
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Zhaojun Li
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China; College of Life Science, Shandong Normal University, Jinan 250014, Shandong, China
Qian Tian
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China
Xuxiao Zong
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Corresponding authors.
Hanfeng Ding
Shandong Center of Crop Germplasm Resources, Shandong Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, Shandong, China; College of Life Science, Shandong Normal University, Jinan 250014, Shandong, China; Corresponding authors.
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 bp 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 (45.29%) 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.
