Next-Generation-Sequencing-Based Simple Sequence Repeat (SSR) Marker Development and Linkage Mapping in Lentil (Lens culinaris L.)

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dc.authoridBektas, Harun/0000-0002-4397-4089
dc.authoridTopu, Mustafa/0000-0001-9654-3891
dc.authoridsesiz, ugur/0000-0003-1234-4276
dc.authoridOzkan, Hakan/0000-0003-3530-2626
dc.contributor.authorTopu, Mustafa
dc.contributor.authorSesiz, Ugur
dc.contributor.authorBektas, Harun
dc.contributor.authorToklu, Faruk
dc.contributor.authorOzkan, Hakan
dc.date.accessioned2024-12-24T19:33:42Z
dc.date.available2024-12-24T19:33:42Z
dc.date.issued2023
dc.departmentSiirt Üniversitesi
dc.description.abstractSimple Summary Although lentil is not as popular as other legumes, it is a climate-resilient legume crop because of its high protein content, nitrogen fixation, and abiotic stress tolerance ability. Even though it can be grown on almost every continent and is distributed globally, the use of existing genetic diversity in marker-assisted selection is still limited. In this study, novel SSR markers needed in lentil were identified using a next-generation sequencing approach. In this study, we created a ready-to-use SSR library for genetic diversity studies and breeding and evaluated the effectiveness of the obtained SSR markers in a recombinant inbred line (RIL) population. Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil (Lens culinaris) breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and diversity of SSR markers in lentil is limited. We used next-generation sequencing (NGS) technology to develop SSR markers in lentil. NGS allowed us to identify regions of the lentil genome that contained SSRs. Illumina Hiseq-2000 sequencing of the lentil genotype Karacadag resulted in 1,727,734 sequence reads comprising more than 48,390 Mb, and contigs were mined for SSRs, resulting in the identification of a total of 8697 SSR motifs. Among these, dinucleotide repeats were the most abundant (53.38%), followed by trinucleotides (30.38%), hexanucleotides (6.96%), tetranucleotides (6.59%), and pentanucleotides (3.19%). The most frequent repeat in dinucleotides was the TC (21.80%), followed by the GA (17.60%). A total of 2000 primer pairs were designed from these motifs, and 458 SSR markers were validated following their amplified PCR products. A linkage map was constructed using these new SSRs with high linkage disequilibrium (209) and previously known SSRs (11). The highest number of SSR markers (43) was obtained in LG2, while the lowest number of SSR markers (19) was obtained in LG7. The longest linkage group (LG) was LG2 (86.84 cM), whereas the shortest linkage group was LG7 (53.46 cM). The average length between markers ranged from 1.86 cM in LG1 to 2.81 cM in LG7, and the map density was 2.16 cM. The developed SSRs and created linkage map may provide useful information and offer a new library for genetic diversity analyses, linkage mapping studies, and lentil breeding programs.
dc.description.sponsorship[114O562]
dc.description.sponsorshipThis research was funded by TUBITAK-TOVAG (grant number 114O562).
dc.identifier.doi10.3390/life13071579
dc.identifier.issn2075-1729
dc.identifier.issue7
dc.identifier.pmid37511954
dc.identifier.scopus2-s2.0-85166335881
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.3390/life13071579
dc.identifier.urihttps://hdl.handle.net/20.500.12604/8227
dc.identifier.volume13
dc.identifier.wosWOS:001036094100001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherMdpi
dc.relation.ispartofLife-Basel
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241222
dc.subjectlentil
dc.subjectLens culinaris
dc.subjectSSR development
dc.subjectlinkage map
dc.subjectnext-generation sequencing
dc.titleNext-Generation-Sequencing-Based Simple Sequence Repeat (SSR) Marker Development and Linkage Mapping in Lentil (Lens culinaris L.)
dc.typeArticle

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