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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Publications at this Location » Publication #314770
Title: Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses

Author
item ALI, L - Universidad De Cordoba
item AZAM, SARWAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item RUBIO, JOSE - Venta Del Llano Ifapa Center
item KUDAPA, HIMABINDU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item MADRID, EVA - Institute For Sustainable Agriculture
item VARSHNEY, R - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item CASTRO, PATRICIA - Former ARS Employee
item Chen, Weidong
item GIL, JUAN - Universidad De Cordoba
item MILAN, TERESA - Universidad De Cordoba

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2015
Publication Date: 7/1/2015
Citation: Ali, L., Azam, S., Rubio, J., Kudapa, H., Madrid, E., Varshney, R.K., Castro, P., Chen, W., Gil, J., Milan, T. 2015. Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses. Euphytica. 204:473-485.

Interpretive Summary: Chickpea is a very important grain legume in the world. It may have either erect or prostate growth habit, which is an important trait for yield and harvest easiness in industrialized countries. However, the genetic control of this growth habit is unknown. In order to investigate the gene or QTL that control the erect/prostate growth habit, a recombinant inbred line population derived from an interspecific cross (ILC72 × Cr5-10) was used to develop a pair of near-isogenic lines for erect vs. prostate habit. Employing 52 molecular markers distributed over different linkage groups of the chickpea genetic map revealed polymorphisms in two linkage groups (CaLG1 and CaLG3), and association between markers and growth habit was detected using simple linear regression based on a previous database. One RAPD marker (OPAD091053) on CaLG1 explained up to 15.4% of the total phenotypic variation for growth habit and it was developed into a more user-friendly SCAR marker (SCAD091053). And new molecular markers were developed on DNA regions adjacent to this SCAR marker, and a new QTL was identified on CaLG1, which explained 24.6% and 23.4% of the phenotypic variation in two consecutive years. The markers were also verified in a separate recombinant inbred population. They could be considered as candidate genes and after further confirmation could be employed in chickpea breeding programs.

Technical Abstract: A recombinant inbred line population (RIP-9) derived from an interspecific cross (ILC72 × Cr5-10) was evaluated for growth habit during two years (2003 and 2004). This RIP was used to develop a pair of near isogenic lines (NILs) for erect vs prostrate growth habit in chickpea. Molecular characterization of the identified pair of NILs was performed using 52 sequence tagged microsatellite site (STMS) markers distributed over different chickpea linkage groups (CaLG) of the genetic map. It revealed polymorphic markers in CaLG1 and CaLG3. Starting from a previous data base simple linear regression was applied to detect association between markers and growth habit. The RAPD (random amplified polymorphic DNA) marker OPAD091053 mapped on CaLG1 explained the highest percentage (maximum 15.4%) of the total phenotypic variation for growth habit and it was used to develop a SCAR (sequence characterized amplified region) marker (SCAD091053). New markers were developed from sequences surrounding SCAD091053 in the physical map. QTL (quantitative trait loci) analysis revealed a new QTL (QTLHg2) in CaLG1. The Indel marker (deletion/insertion) Indel 3 and the predicted gene Ca_07000 (14,5 Mb of Ca1) and (15,3 Mb of Ca1) had the highest LOD values explaining 24.6% and 23.4% of the phenotypic variation in years 2003 and 2004, respectively. To confirm these results, another RIP (RIP-5) derived from an intraspecific cross (WR315 × ILC3279) and segregating for erect vs semi-erect growth habit was employed. RIP-5 allowed mapping the gene (Hg2/hg2) on CaLG1 that was flnaked by two Indel markers (Indel 1 and Indel 2) in the range of 12,3 and 16,2 Mb. So, Hg2/hg2 gene corresponds to QTLHg2 region. The annotated genes Ca_07000 and Ca_06999 were homologues to predicted zinc finger genes in Glycine max and Pisum sativum, respectively. Hence, they could be considered as possible candidate genes.