Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea

Soren, Khela Ram; Madugula, Praveen; Kumar, Neeraj; Barmukh, Rutwik; Sengar, Meenu Singh; Bharadwaj, Chellapilla; Sharma, Parbodh Chander; Singh, Sarvjeet; Bhandari, Aditi; Singh, Jogendra; Sanwal, Satish Kumar; Pal, Madan; P.R., Sneha Priya; Mann, Anita; Sagurthi, Someswar Rao; PS, Shanmugavadivel; Siddique, Kadambot H.M.; Singh, Narendra Pratap; Roorkiwal, Manish; Varshney, Rajeev K

doi:10.3390/ijms21145058

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Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom^®CicerSNP Array in Chickpea

^1,†,

^2,†,

^3,†

^2,4

¹,

Chellapilla Bharadwaj

Parbodh Chander Sharma

⁵,

⁶

²,

⁵

⁵,

³,

³,

⁵

Someswar Rao Sagurthi

⁴

Shanmugavadivel PS

Kadambot H.M. Siddique

⁷,

Narendra Pratap Singh

¹,

Manish Roorkiwal

^2,7,*

and

Rajeev K Varshney

^2,7,*

ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur UP 208024, India

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India

Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), Delhi 110012, India

⁴

Department of Genetics, Osmania University, Hyderabad 500007, India

⁵

ICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal 132001, India

⁶

Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana 141004, India

⁷

The UWA Institute of Agriculture, The University of Western Australia, Perth WA 6009, Australia

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2020, 21(14), 5058; https://doi.org/10.3390/ijms21145058

Received: 4 June 2020 / Revised: 10 July 2020 / Accepted: 14 July 2020 / Published: 17 July 2020

(This article belongs to the Special Issue Mechanisms of Drought, Temperature and Salinity Tolerance in Plants)

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Abstract

Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom^®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance. View Full-Text

Keywords: chickpea; salinity; quantitative trait loci; stress susceptibility index (SSI); stress tolerance index (STI); candidate genes

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Soren, K.R.; Madugula, P.; Kumar, N.; Barmukh, R.; Sengar, M.S.; Bharadwaj, C.; Sharma, P.C.; Singh, S.; Bhandari, A.; Singh, J.; Sanwal, S.K.; Pal, M.; P.R., S.P.; Mann, A.; Sagurthi, S.R.; PS, S.; Siddique, K.H.M.; Singh, N.P.; Roorkiwal, M.; Varshney, R.K. Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom^®CicerSNP Array in Chickpea. Int. J. Mol. Sci. 2020, 21, 5058. https://doi.org/10.3390/ijms21145058

AMA Style

Soren KR, Madugula P, Kumar N, Barmukh R, Sengar MS, Bharadwaj C, Sharma PC, Singh S, Bhandari A, Singh J, Sanwal SK, Pal M, P.R. SP, Mann A, Sagurthi SR, PS S, Siddique KHM, Singh NP, Roorkiwal M, Varshney RK. Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom^®CicerSNP Array in Chickpea. International Journal of Molecular Sciences. 2020; 21(14):5058. https://doi.org/10.3390/ijms21145058

Chicago/Turabian Style

Soren, Khela Ram, Praveen Madugula, Neeraj Kumar, Rutwik Barmukh, Meenu Singh Sengar, Chellapilla Bharadwaj, Parbodh Chander Sharma, Sarvjeet Singh, Aditi Bhandari, Jogendra Singh, Satish Kumar Sanwal, Madan Pal, Sneha Priya P.R., Anita Mann, Someswar Rao Sagurthi, Shanmugavadivel PS, Kadambot H.M. Siddique, Narendra Pratap Singh, Manish Roorkiwal, and Rajeev K Varshney. 2020. "Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom^®CicerSNP Array in Chickpea" International Journal of Molecular Sciences 21, no. 14: 5058. https://doi.org/10.3390/ijms21145058

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Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom^®CicerSNP Array in Chickpea

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