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

cg.contactdinghanfeng@shandong.cnen_US
cg.contributor.centerInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.contributor.centerChinese Academy of Agricultural Sciences, Institute of Crop Science - CAAS-ICSen_US
cg.contributor.centerShandong Research Station of Crop Gene Resource & Germplasm Enhancementen_US
cg.contributor.centerShandong Normal University - SDNUen_US
cg.contributor.funderInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.contributor.projectCommunication and Documentation Information Services (CODIS)en_US
cg.contributor.project-lead-instituteInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.creator.idSarker, Ashutosh: 0000-0002-9074-4876en_US
cg.identifier.doihttps://dx.doi.org/10.1016/j.cj.2020.04.007en_US
cg.isijournalISI Journalen_US
cg.issn2214-5141en_US
cg.issue6en_US
cg.journalThe Crop Journalen_US
cg.subject.agrovoclentilsen_US
cg.subject.agrovoclentilen_US
cg.volume8en_US
dc.contributorYang, Taoen_US
dc.contributorLiu, Rongen_US
dc.contributorLi, Nanaen_US
dc.contributorWang, Xiaomuen_US
dc.contributorSarker, Ashutoshen_US
dc.contributorZhang, Xiaodongen_US
dc.contributorLi, Runfangen_US
dc.contributorPu, Yanyanen_US
dc.contributorLi, Guanen_US
dc.contributorHuang, Yuningen_US
dc.contributorJi, Yishanen_US
dc.contributorLi, Zhaojunen_US
dc.contributorTian, Qianen_US
dc.contributorZong, Xuxiaoen_US
dc.contributorDing, Hanfengen_US
dc.creatorwang, Dong-Fengen_US
dc.date.accessioned2021-08-18T22:42:20Z
dc.date.available2021-08-18T22:42:20Z
dc.description.abstractLentil (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.en_US
dc.formatPDFen_US
dc.identifierhttps://mel.cgiar.org/reporting/downloadmelspace/hash/5572fdcd8266dc90553b1f136871b618/v/7c77d12fdbd06dca64afeed111f83520en_US
dc.identifier.citationDong-Feng 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. (1/12/2020). RNA-Seq analysis and development of SSR and KASP markers in lentil (Lens culinaris Medikus subsp. culinaris). The Crop Journal, 8 (6), pp. 953-965.en_US
dc.identifier.statusOpen accessen_US
dc.identifier.urihttps://hdl.handle.net/20.500.11766/13575
dc.languageenen_US
dc.publisherElsevieren_US
dc.rightsCC-BY-NC-ND-4.0en_US
dc.sourceThe Crop Journal;8,(2020) Pagination 953-965en_US
dc.subjectrna-seqen_US
dc.subjectest-ssren_US
dc.subjectgenetic diversityen_US
dc.subjectkaspen_US
dc.titleRNA-Seq analysis and development of SSR and KASP markers in lentil (Lens culinaris Medikus subsp. culinaris)en_US
dc.typeJournal Articleen_US
dcterms.available2020-06-19en_US
dcterms.extent953-965en_US
dcterms.issued2020-12-01en_US
mel.impact-factor4.407en_US

Files