title: Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.).
abstract: In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Mahendar
authors.initials: M
authors.lastname: Thudi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Annapurna
authors.initials: A
authors.lastname: Chitikineni
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Roorkiwal
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Jian
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Dadakhalandar
authors.initials: D
authors.lastname: Doddamani
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Pooran M
authors.initials: PM
authors.lastname: Gaur
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Rathore
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Samineni
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Dawen
authors.initials: D
authors.lastname: Xu
authors.affiliation: All India Coordinated Research Project (AICRP) on Chickpea, Indian Council of Agricultural Research (ICAR), New Delhi, India.|Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India.
authors.forename: Narendra P
authors.initials: NP
authors.lastname: Singh
authors.affiliation: Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India.
authors.forename: Sushil K
authors.initials: SK
authors.lastname: Chaturvedi
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Gengyun
authors.initials: G
authors.lastname: Zhang
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Visva-Bharati, Santiniketan, India.
authors.forename: Swapan K
authors.initials: SK
authors.lastname: Datta
authors.affiliation: BGI - Shenzhen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000383:Agriculture; D001947:Breeding; D029863:Cicer / Q000235:genetics*; D060467:Disease Resistance / Q000235:genetics; D055864:Droughts; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D006239:Haplotypes / Q000235:genetics; D054643:INDEL Mutation / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic; D013997:Time Factors