Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Sarı, Duygu; Sari, Hatice; İkten, Cengiz; Toker, Cengiz

doi:10.1038/s41598-023-37268-w

Cited by 3 publications

(1 citation statement)

References 87 publications

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“…The reliable, highly reproducible, and low-cost nature of genotyping assays using SSR markers make it one of the simplest and most suitable molecular tools for MAS in many crops [37,38]. Simple codominant inheritance, reproducibility, bi-or multi-allelic nature, and abundant genomic distribution represent desirable genetic attributes of sequencebased robust SSR markers [39].…”

Section: Introductionmentioning

confidence: 99%

SSR Genotyping and Marker–Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

Mazkirat,

Baitarakova,

Kudaybergenov

et al. 2023

Biomolecules

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Genetic diversity and marker–trait association with yield-related components were assessed in 39 chickpea accessions from a germplasm collection with either spring or autumn-sown seeds in South-Eastern Kazakhstan. Chickpea accessions originated from Azerbaijan, Germany, Kazakhstan, Moldova, Russia, Türkiye, Ukraine, Syria, and the International Center for Agricultural Research in the Dry Areas (ICARDA). Eleven SSR markers were used for molecular genotyping. Yield and yield components were evaluated in nine traits in experiments with spring and autumn seed sowing. The number of alleles of polymorphic markers varied from 2 to 11. The greatest polymorphism was found in the studied chickpea genotypes using SSR marker TA22 (11 alleles), while NCPGR6 and NCPGR12 markers were monomorphic. In the studied chickpea accessions, unique alleles of the SSR loci TA14, TA46, TA76s, and TA142 were found that were not previously described by other authors. An analysis of correlation relationships between yield-related traits in chickpea revealed the dependence of yield on plant height, branching, and the setting of a large number of beans. These traits showed maximal values in experiments with chickpea plants from autumn seed sowing. An analysis of the relationship between the SSR markers applied and morphological yield-related traits revealed several informative markers associated with important traits, such as plant height, height to first pod, number of branches, number of productive nodes, number of pods per plant, hundred seed weight, seed weight per plant, and seed yield.

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Section: Introductionmentioning

confidence: 99%

SSR Genotyping and Marker–Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

Mazkirat,

Baitarakova,

Kudaybergenov

et al. 2023

Biomolecules

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INTEGRATION OF NOVEL SSR MARKERS INTO THE LENTIL (Lens culinaris Medik.) GENOME

Wakimwayi Koboyi,

Bakır

2024

Turkish Journal of Field Crops

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The development of Simple Sequence Repeat markers (SSRs) for lentil has played a pivotal role in enhancing the comprehension of the lentil genome through genetic mapping. The study aimed to determine the relative positions of newly developed microsatellites to the lentil genome using an F7-derived Recombinant Inbred Lines population (RIL) of 71 individuals developed from a cross between Eston and PI320937. Molecular analysis was performed with 100 newly developed lentil SSR markers and a linkage map was constructed using MapMaker/EXP 3.0b and MapChart 2.2 software. Among the 100 SSR markers, 12 markers exhibited polymorphism, 54 markers were identified as monomorphic, and 34 markers remained unamplified. While 10 out of the 12 polymorphic markers successfully integrated into two linkage groups, covering a cumulative length of 19.2cM, two markers remained unlinked. Linkage group-1, comprised of 8 markers, spanned 4.8cM, and linkage group-2 extended over a length of 14.4cM with two markers. Despite only partially representing 2 out of the 7 chromosomes in the lentil genome, this map holds promise for future mapping studies. Through the addition of markers, it could facilitate marker-assisted selection and the identification of QTLs associated with specific agronomic traits.

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Agarose-Resolvable SSR Markers Based on ddRADSeq in Chickpea

Sarı

2024

Black Sea Journal of Agriculture

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Exploitation of genetic diversity is essential for sustainable crop production. Molecular markers have potential to reach these goals in more rapid and efficient manner. Simple sequence repeats (SSRs) are one of the most popular molecular markers in breeding studies due to their co-dominant inheritance, abundance in the genome, multi-allelic and reproducible nature. Here, we developed genomic SSR markers from chickpea with the use of ddRADSeq data. 1,396 SSR regions with an average of 530 SSR/Mb in the whole genome were successfully identified. Considering different types of repeats, dinucleotides were the most frequent type accounting for 62.03% of the total SSR regions identified, followed by trinucleotides (25.50%) and tetranucleotides (4.58%). The AT/TA motif was greatly characterized among dinucleotide repeats, and it was also the most common type in the chickpea genome accounting for 36.5% of the total SSR regions identified, followed by AG/GA (139) and TC/CT (135) among dinucleotide motifs. Considering their genomic distribution and simple visualization on agarose gels, we examined SSR regions of 10 bp and longer for identification of SSR markers. A total of 10 SSR markers were successfully designed and resulted in successful polymorphic bands among chickpea genotypes. Consequently, the results show that ddRADSeq is effective for marker development and these markers might be valuable for biodiversity studies, marker-assisted selection (MAS) and linkage map construction in chickpea.

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Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Cited by 3 publications

References 87 publications

SSR Genotyping and Marker–Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

SSR Genotyping and Marker–Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

INTEGRATION OF NOVEL SSR MARKERS INTO THE LENTIL (Lens culinaris Medik.) GENOME

Agarose-Resolvable SSR Markers Based on ddRADSeq in Chickpea

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