Research Article
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Agarose-Resolvable SSR Markers Based on ddRADSeq in Chickpea

Year 2024, , 399 - 406, 15.07.2024

Duygu Sarı

https://doi.org/10.47115/bsagriculture.1438678

Abstract

Exploitation of genetic diversity is essential for sustainable crop production. Molecular markers have potential to reach these goals in more rapid and efficient manner. 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.

Keywords

Chickpea ddRADSeq Marker SSR Sequencing

Supporting Institution

Akdeniz University Scientific Research Project Coordination Unit

Project Number

FBA-2022-6106

References

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  • Ahmadi AJ, Ahmadikhah A. 2022. Occurrence of simple sequence repeats in cDNA sequences of safflower (Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues. Front Plant Sci, 13: 991107.
  • Amirmoradi B, Talebi R, Karami E. 2012. Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst Evol, 298: 1679-1688.
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  • Cloutier S, Niu Z, Datla R, Duguid S. 2009. Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet, 119: 53-63.
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  • Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo M, Gu YQ. 2008. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics, 8: 135-147.
  • Iruela M, Rubio J, Cubero JI, Gil J, Milan T. 2002. Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theor Appl Genet, 104: 643-651.
  • Jaganathan D, Thudi M, Kale S, Azam S, Roorkiwal M, Gaur PM, Kishor PB, Nguyen H, Sutton T, Varshney RK. 2015. Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea. Mol Genet Genomic, 290: 559-571.
  • Jha UC, Kole PC, Singh NP. 2019. QTL mapping for heat stress tolerance in chickpea (Cicer arietinum L.). Legume Res, 44(4): 382-387.
  • Kaur R, Sharma N, Raina R. 2015. Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana. Turk J Agric For, 39(3): 439-450.
  • Khajuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M, Parida SK, Bhatia S. 2015. Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea. PLoS One, 10(5): e0125583.
  • Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. 2015. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Front Plant Sci, 6: 162.
  • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods, 9: 357-359.
  • Lawson MJ, Zhang L. 2006. Distinct patterns of SSR distribution in the Arabidopsis thalianaand rice genomes. Genome Biol, 7(2): 1-11.
  • Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui, Y, Cheng F, Wang X, Wu J. 2013. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet, 126: 231-239.
  • Nguyen TT, Taylor PWJ, Redden RJ, Ford R. 2004. Genetic diversity estimates in Cicer using AFLP analysis. Plant Breed, 123(2): 173-179.
  • Parida SK, Dalal V, Singh AK, Singh NK, Mohapatra T. 2009. Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. BMC Genomics, 10: 1-14.
  • Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M. 2015. Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Front Plant Sci, 6: 645.
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  • Roorkiwal M, Nayak SN, Thudi M, Upadhyaya HD, Brunel D, Mournet P, This D, Sharma PC, Varshney RK. 2014. Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers. Front Plant Sci, 5: 248.
  • Sakiyama NS, Ramos HCC, Caixeta ET, Pereira MG. 2014. Plant breeding with marker-assisted selection in Brazil. Crop Breed Appl Biotechnol, 14: 54-60.
  • Sari D, Sari H, Eker T, Ikten C, Uzun B, Toker C. 2022. Intraspecific versus interspecific crosses for superior progeny in Cicer species. Crop Sci, 62(6): 2122-2137.
  • Sari D, Sari H, Ikten C, Toker C. 2023. Genome-wide discovery of dinucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz. Sci Rep, 13(1): 10351.
  • Sethy NK, Shokeen B, Edwards KJ, Bhatia S. 2006. Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet, 112: 1416-1428.
  • Seyedimoradi H, Talebi R, Kanouni H, Naji AM, Karami E. 2020. Genetic diversity and population structure analysis of chickpea (Cicer arietinum L.) advanced breeding lines using whole-genome DArTseq-generated SilicoDArT markers. Braz J Bot, 43(3): 541-549.
  • Shan F, Clarke HJ, Yan G, Plummer JA, Siddique KHM. 2007. Identification of duplicates and fingerprinting of primary and secondary wild annual Cicer gene pools using AFLP markers. Genet Resour Crop Evol, 54: 519-527.
  • Singh A, Devarumath RM, Ramarao S, Singh VP, Raina SN. 2008. Assessment of genetic diversity, and phylogenetic relationships based on ribosomal DNA repeat unit length variation and Internal Transcribed Spacer (ITS) sequences in chickpea (Cicer arietinum) cultivars and its wild species. Genet Resour Crop Evol, 55: 65-79.
  • Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. 2023. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol, 21: 640-656.
  • Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K. 2010. Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol Breed, 25: 359-364.
  • Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. 2023. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep, 13(1): 10919.
  • Sonah H, Deshmukh RK, Sharma A, Singh VP, Gupta DK, Gacche RN, Rana JC, Singh NK, Sharma TR. 2011. Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. Plos One, 6(6): e21298.
  • Srivastava R, Singh M, Bajaj D, Parida SK. 2016. A high-resolution InDel (insertion–deletion) markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea. Front Plant Sci, 7: 1362.
  • Sudupak MA. 2004. Inter and intra-species Inter Simple Sequence Repeat (ISSR) variations in the genus Cicer. Euphytica, 135: 229-238.
  • Talebi R, Fayaz F, Mardi M, Pirsyedi SM, Naji AM. 2008. Genetic relationships among chickpea (Cicer arietinum) elite lines based on RAPD and agronomic markers. Int J Agric Biol, 10: 47-47.
  • Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. 2009. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol, 9(1): 1-12.
  • Thudi M, Khan AW, Kumar V, Gaur PM, Katta K, Garg V, Roorkiwal M, Samineni S, Varshney RK. 2016. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biol, 16(1): 53–64.
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Year 2024, , 399 - 406, 15.07.2024

Duygu Sarı

https://doi.org/10.47115/bsagriculture.1438678

Abstract

Project Number

FBA-2022-6106

References

  • Abuzayed MA, Goktay M, Allmer J, Doganlar S, Frary A. 2017. Development of genomic simple sequence repeat markers in faba bean by next-generation sequencing. Plant Mol Biol Rep, 35: 61-71.
  • Aggarwal H, Rao A, Kumar A, Singh J, Rana JS, Naik PK, Chhokar V. 2015. Assessment of genetic diversity among 125 cultivars of chickpea (Cicer arietinum L.) of Indian origin using ISSR markers. Turk J Bot, 39: 218-226.
  • Ahmad Z, Nisar M, Mumtaz AS, Ghafoor A, Ali S. 2014. SSR markers linked to seed size and seed weight in local and exotic chickpea germplasm reported from Pakistan. Pak J Bot, 46(6): 2113-2120.
  • Ahmadi AJ, Ahmadikhah A. 2022. Occurrence of simple sequence repeats in cDNA sequences of safflower (Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues. Front Plant Sci, 13: 991107.
  • Amirmoradi B, Talebi R, Karami E. 2012. Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst Evol, 298: 1679-1688.
  • Bhati J, Chandrasekaran H, Chand S. 2015. In silico EST mining of Fabaceae species. Indian J Biotechnol, 14: 461-468.
  • Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y. 2010. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics, 11: 569
  • Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17): i884-i890.
  • Cloutier S, Niu Z, Datla R, Duguid S. 2009. Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet, 119: 53-63.
  • Cui C, Mei H, Liu Y, Zhang H, Zheng Y. 2017. Genetic diversity, population structure, and linkage disequilibrium of an association-mapping panel revealed by genome-wide SNP markers in sesame. Front Plant Sci, 8: 1189.
  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet, 12: 499-510.
  • Doyle JJ, Doyle JL. 1990. A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12: 13-15.
  • FAO. 2022. FAO Statistical Databases (FAOSTAT). URL: https://www.fao.org/faostat/en/#data/QCL. (accessed date: February 26, 2023).
  • Freese NH, Norris DC, Loraine AE. 2016. Integrated genome browser: visual analytics platform for genomics. Bioinformatics, 32(14): 2089-2095.
  • Garrison E, Marth G. 2012. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907.
  • Gaur R, Aza S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S. 2012. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res, 19: 357-73.
  • Gaur PM, Singh MK, Samineni S, Sajja SB, Jukanti AK, Kamatam S, Varshney RK. 2016. Inheritance of protein content and its relationships with seed size, grain yield and other traits in chickpea. Euphytica, 209: 253-260.
  • Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong EE. 2016. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics, 17: 1-6.
  • Gong YM, Xu SC, Mao WH, Hu QZ, Zhang GW, Ding J, Li YD. 2010. Developing new SSR markers from ESTs of pea (Pisum sativum L.). J. Zhejiang Univ Sci B, 11: 702-707.
  • Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF. 2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant J, 50(6): 995-1006.
  • Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Prakash AB, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR, May GD, Varshney RV. 2011. Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.) Theor Appl Genet, 122: 1577-89.
  • Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. 2021. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol, 19(1): 1-26.
  • Herridge DF, Rupela OP, Serraj R, Beck DP. 1993. Screening techniques and improved biological nitrogen fixation in cool season food legumes. Euphytica, 73(1): 95-108.
  • Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S. 2007. Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res, 14(6): 271-281.
  • Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo M, Gu YQ. 2008. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics, 8: 135-147.
  • Iruela M, Rubio J, Cubero JI, Gil J, Milan T. 2002. Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theor Appl Genet, 104: 643-651.
  • Jaganathan D, Thudi M, Kale S, Azam S, Roorkiwal M, Gaur PM, Kishor PB, Nguyen H, Sutton T, Varshney RK. 2015. Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea. Mol Genet Genomic, 290: 559-571.
  • Jha UC, Kole PC, Singh NP. 2019. QTL mapping for heat stress tolerance in chickpea (Cicer arietinum L.). Legume Res, 44(4): 382-387.
  • Kaur R, Sharma N, Raina R. 2015. Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana. Turk J Agric For, 39(3): 439-450.
  • Khajuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M, Parida SK, Bhatia S. 2015. Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea. PLoS One, 10(5): e0125583.
  • Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. 2015. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Front Plant Sci, 6: 162.
  • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods, 9: 357-359.
  • Lawson MJ, Zhang L. 2006. Distinct patterns of SSR distribution in the Arabidopsis thalianaand rice genomes. Genome Biol, 7(2): 1-11.
  • Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui, Y, Cheng F, Wang X, Wu J. 2013. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet, 126: 231-239.
  • Nguyen TT, Taylor PWJ, Redden RJ, Ford R. 2004. Genetic diversity estimates in Cicer using AFLP analysis. Plant Breed, 123(2): 173-179.
  • Parida SK, Dalal V, Singh AK, Singh NK, Mohapatra T. 2009. Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. BMC Genomics, 10: 1-14.
  • Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M. 2015. Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Front Plant Sci, 6: 645.
  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS One, 7(5): e37135.
  • Roorkiwal M, Nayak SN, Thudi M, Upadhyaya HD, Brunel D, Mournet P, This D, Sharma PC, Varshney RK. 2014. Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers. Front Plant Sci, 5: 248.
  • Sakiyama NS, Ramos HCC, Caixeta ET, Pereira MG. 2014. Plant breeding with marker-assisted selection in Brazil. Crop Breed Appl Biotechnol, 14: 54-60.
  • Sari D, Sari H, Eker T, Ikten C, Uzun B, Toker C. 2022. Intraspecific versus interspecific crosses for superior progeny in Cicer species. Crop Sci, 62(6): 2122-2137.
  • Sari D, Sari H, Ikten C, Toker C. 2023. Genome-wide discovery of dinucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz. Sci Rep, 13(1): 10351.
  • Sethy NK, Shokeen B, Edwards KJ, Bhatia S. 2006. Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet, 112: 1416-1428.
  • Seyedimoradi H, Talebi R, Kanouni H, Naji AM, Karami E. 2020. Genetic diversity and population structure analysis of chickpea (Cicer arietinum L.) advanced breeding lines using whole-genome DArTseq-generated SilicoDArT markers. Braz J Bot, 43(3): 541-549.
  • Shan F, Clarke HJ, Yan G, Plummer JA, Siddique KHM. 2007. Identification of duplicates and fingerprinting of primary and secondary wild annual Cicer gene pools using AFLP markers. Genet Resour Crop Evol, 54: 519-527.
  • Singh A, Devarumath RM, Ramarao S, Singh VP, Raina SN. 2008. Assessment of genetic diversity, and phylogenetic relationships based on ribosomal DNA repeat unit length variation and Internal Transcribed Spacer (ITS) sequences in chickpea (Cicer arietinum) cultivars and its wild species. Genet Resour Crop Evol, 55: 65-79.
  • Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. 2023. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol, 21: 640-656.
  • Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K. 2010. Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol Breed, 25: 359-364.
  • Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. 2023. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep, 13(1): 10919.
  • Sonah H, Deshmukh RK, Sharma A, Singh VP, Gupta DK, Gacche RN, Rana JC, Singh NK, Sharma TR. 2011. Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. Plos One, 6(6): e21298.
  • Srivastava R, Singh M, Bajaj D, Parida SK. 2016. A high-resolution InDel (insertion–deletion) markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea. Front Plant Sci, 7: 1362.
  • Sudupak MA. 2004. Inter and intra-species Inter Simple Sequence Repeat (ISSR) variations in the genus Cicer. Euphytica, 135: 229-238.
  • Talebi R, Fayaz F, Mardi M, Pirsyedi SM, Naji AM. 2008. Genetic relationships among chickpea (Cicer arietinum) elite lines based on RAPD and agronomic markers. Int J Agric Biol, 10: 47-47.
  • Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. 2009. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol, 9(1): 1-12.
  • Thudi M, Khan AW, Kumar V, Gaur PM, Katta K, Garg V, Roorkiwal M, Samineni S, Varshney RK. 2016. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biol, 16(1): 53–64.
  • Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res, 35: W71-W74.
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There are 62 citations in total.

Details

Primary Language English
Subjects Agricultural Engineering (Other)
Journal Section Research Articles
Authors

Duygu Sarı 0000-0002-7909-2627

Project Number FBA-2022-6106
Publication Date July 15, 2024
Submission Date February 17, 2024
Acceptance Date July 3, 2024
Published in Issue Year 2024

Cite

APA Sarı, D. (2024). Agarose-Resolvable SSR Markers Based on ddRADSeq in Chickpea. Black Sea Journal of Agriculture, 7(4), 399-406. https://doi.org/10.47115/bsagriculture.1438678

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