RNA-Seq analysis and development of SSR and KASP markers in lentil (Lens culinaris Medikus subsp. culinaris)

Publication Overview
TitleRNA-Seq analysis and development of SSR and KASP markers in lentil (Lens culinaris Medikus subsp. culinaris)
AuthorsWang D, Yang T, Liu R, Li N, Wang X, Sarker A, Zhang X, Li R, Pu Y, Li G, Huang Y, Ji Y, Li Z, Tian Q, Zong X, Ding H
TypeJournal Article
Journal NameThe Crop Journal
Volume8
Year2020
Page(s)953-965
CitationWang D, Yang T, Liu R, Li N, Wang X, Sarker A, Zhang X, Li R, Pu Y, Li G, Huang Y, Ji Y, Li Z, Tian Q, Zong X, Ding H. RNA-Seq analysis and development of SSR andKASP markers in lentil (Lens culinaris Medikus subsp. culinaris). The Crop Journal. 2020; 8:953-965.

Abstract

Lentil (Lens culinarisMedikus subsp.culinaris,2n= 14) is a cool-season legume with highproduction potential for multiple uses. However, limited molecular research has beenconducted in this species owing to its large genome, which impedes the generation ofgenome sequences and the development of molecular markers. In this study, more than 1.37billion filtered clean reads were collected by RNA-Seq of six diverse lentil accessions and217,836 transcripts and 161,095 unigenes werede novoassembled, yielding respectively 257.1and 240.6 million nucleotides. The mean transcript length was 1180 bp and the N50 and N90lengths were respectively 2075 and 479 bp. The mean length of the unigenes was 1494 bp andtheir N50 and N90 values were respectively 2203 and 714 bp. The unigenes were annotatedagainst seven databases. TheFLOWERING LOCUS T(FT) gene homolog in lentil showed highprotein sequence similarity to theFTgene homologs of pea and alfalfa. On the basis of theRNA-Seq analysis, 26,449 EST-SSR markers were designedin silico, and 276 preliminarilyscreened markers were selected to evaluate polymorphism in 94 diverse lentil accessions. Intotal, 125 (45.29%) of 276 EST-SSR markers were found to be polymorphic. A total of 130,073SNP loci were detected and 78 (61.41%) of 127 SNPs were successfully converted to KASPmarkers. Population genetic analyses of the lentil accessions with EST-SSR and KASP markersrevealed similar genetic structures, suggesting that the RNA-Seq-generated resources and thedeveloped markers are reliable for use in molecular marker-assisted breeding of lentil.
Features
This publication contains information about 252 features:
Feature NameUniquenameType
SCCGR_P001SCCGR_P001genetic_marker
SCCGR_P002SCCGR_P002genetic_marker
SCCGR_P005SCCGR_P005genetic_marker
SCCGR_P009SCCGR_P009genetic_marker
SCCGR_P013SCCGR_P013genetic_marker
SCCGR_P014SCCGR_P014genetic_marker
SCCGR_P015SCCGR_P015genetic_marker
SCCGR_P017SCCGR_P017genetic_marker
SCCGR_P021SCCGR_P021genetic_marker
SCCGR_P032SCCGR_P032genetic_marker
SCCGR_P033SCCGR_P033genetic_marker
SCCGR_P040SCCGR_P040genetic_marker
SCCGR_P041SCCGR_P041genetic_marker
SCCGR_P042SCCGR_P042genetic_marker
SCCGR_P050SCCGR_P050genetic_marker
SCCGR_P051SCCGR_P051genetic_marker
SCCGR_P052SCCGR_P052genetic_marker
SCCGR_P055SCCGR_P055genetic_marker
SCCGR_P062SCCGR_P062genetic_marker
SCCGR_P064SCCGR_P064genetic_marker
SCCGR_P065SCCGR_P065genetic_marker
SCCGR_P067SCCGR_P067genetic_marker
SCCGR_P069SCCGR_P069genetic_marker
SCCGR_P073SCCGR_P073genetic_marker
SCCGR_P078SCCGR_P078genetic_marker

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URLhttps://www.sciencedirect.com/science/article/pii/S2214514120300763