Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Spurthi N. Nayak; Hongyan Zhu; Nicy Varghese; Subhojit Datta; Hong Kyu Choi; Ralf Horres; Ruth Jüngling; Jagbir Singh; P. B.Kavi Kishor; S. Sivaramakrishnan; Dave A. Hoisington; Günter Kahl; Peter Winter; Douglas R. Cook; Rajeev K. Varshney

doi:10.1007/s00122-010-1265-1

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Spurthi N. Nayak, Hongyan Zhu, Nicy Varghese, Subhojit Datta, Hong Kyu Choi, Ralf Horres, Ruth Jüngling, Jagbir Singh, P. B.Kavi Kishor, S. Sivaramakrishnan, Dave A. Hoisington, Günter Kahl, Peter Winter, Douglas R. Cook, Rajeev K. Varshney

Plant and Soil Sciences

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Abstract

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

Original language	English
Pages (from-to)	1415-1441
Number of pages	27
Journal	Theoretical And Applied Genetics
Volume	120
Issue number	7
DOIs	https://doi.org/10.1007/s00122-010-1265-1
State	Published - May 2010

Bibliographical note

Funding Information:
Thanks are due to Prathima Juvvadi, Gudipati Srivani and Abdul Gafoor for their technical assistance. Financial support from Tropical Legume I of Generation Challenge Program (GCP, http://www.generationcp.org ) of CGIAR and National Fund of Indian Council of Agricultural Research of Government of India are gratefully acknowledged. The financial support by National Science Foundation Grant 0110206 to DRC is acknowledged. Council of Scientific and Industrial Research (CSIR), Government of India is acknowledged for providing fellowship to SNN and the Indian Council of Research NATP-HRD program for providing fellowship to SD. We thank Dr. Fred Muehlbauer of the USDA-ARS for providing the chickpea recombinant inbred population and genetic marker data.

ASJC Scopus subject areas

Biotechnology
Agronomy and Crop Science
Genetics

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Nayak, S. N., Zhu, H., Varghese, N., Datta, S., Choi, H. K., Horres, R., Jüngling, R., Singh, J., Kishor, P. B. K., Sivaramakrishnan, S., Hoisington, D. A., Kahl, G., Winter, P., Cook, D. R., & Varshney, R. K. (2010). Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical And Applied Genetics, 120(7), 1415-1441. https://doi.org/10.1007/s00122-010-1265-1

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title = "Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome",

abstract = "This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.",

author = "Nayak, {Spurthi N.} and Hongyan Zhu and Nicy Varghese and Subhojit Datta and Choi, {Hong Kyu} and Ralf Horres and Ruth J{\"u}ngling and Jagbir Singh and Kishor, {P. B.Kavi} and S. Sivaramakrishnan and Hoisington, {Dave A.} and G{\"u}nter Kahl and Peter Winter and Cook, {Douglas R.} and Varshney, {Rajeev K.}",

note = "Funding Information: Thanks are due to Prathima Juvvadi, Gudipati Srivani and Abdul Gafoor for their technical assistance. Financial support from Tropical Legume I of Generation Challenge Program (GCP, http://www.generationcp.org ) of CGIAR and National Fund of Indian Council of Agricultural Research of Government of India are gratefully acknowledged. The financial support by National Science Foundation Grant 0110206 to DRC is acknowledged. Council of Scientific and Industrial Research (CSIR), Government of India is acknowledged for providing fellowship to SNN and the Indian Council of Research NATP-HRD program for providing fellowship to SD. We thank Dr. Fred Muehlbauer of the USDA-ARS for providing the chickpea recombinant inbred population and genetic marker data. ",

year = "2010",

month = may,

doi = "10.1007/s00122-010-1265-1",

language = "English",

volume = "120",

pages = "1415--1441",

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Nayak, SN, Zhu, H, Varghese, N, Datta, S, Choi, HK, Horres, R, Jüngling, R, Singh, J, Kishor, PBK, Sivaramakrishnan, S, Hoisington, DA, Kahl, G, Winter, P, Cook, DR & Varshney, RK 2010, 'Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome', Theoretical And Applied Genetics, vol. 120, no. 7, pp. 1415-1441. https://doi.org/10.1007/s00122-010-1265-1

TY - JOUR

T1 - Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

AU - Nayak, Spurthi N.

AU - Zhu, Hongyan

AU - Varghese, Nicy

AU - Datta, Subhojit

AU - Choi, Hong Kyu

AU - Horres, Ralf

AU - Jüngling, Ruth

AU - Singh, Jagbir

AU - Kishor, P. B.Kavi

AU - Sivaramakrishnan, S.

AU - Hoisington, Dave A.

AU - Kahl, Günter

AU - Winter, Peter

AU - Cook, Douglas R.

AU - Varshney, Rajeev K.

N1 - Funding Information: Thanks are due to Prathima Juvvadi, Gudipati Srivani and Abdul Gafoor for their technical assistance. Financial support from Tropical Legume I of Generation Challenge Program (GCP, http://www.generationcp.org ) of CGIAR and National Fund of Indian Council of Agricultural Research of Government of India are gratefully acknowledged. The financial support by National Science Foundation Grant 0110206 to DRC is acknowledged. Council of Scientific and Industrial Research (CSIR), Government of India is acknowledged for providing fellowship to SNN and the Indian Council of Research NATP-HRD program for providing fellowship to SD. We thank Dr. Fred Muehlbauer of the USDA-ARS for providing the chickpea recombinant inbred population and genetic marker data.

PY - 2010/5

Y1 - 2010/5

N2 - This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

AB - This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

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Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

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