Journal
PLANT SCIENCE
Volume 285, Issue -, Pages 122-131Publisher
ELSEVIER IRELAND LTD
DOI: 10.1016/j.plantsci.2019.04.018
Keywords
Chickpea wild - domestic introgression; Nested association mapping; QTL mapping; GWAS; Bayesian network; Random forest; Machine learning
Categories
Funding
- US National Science Foundation Plant Genome Program [NSF PGRP 1339346]
- United States Agency for International Development under the Feed the Future Program [AID-OAA-A-14-00008]
- Government of Norway through the Global Crop Diversity Trust [CWR14NOR2 3.3 07]
- Russian Scientific Fund [16-16-00007]
- Russian Science Foundation [19-16-11005] Funding Source: Russian Science Foundation
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Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by (similar to)100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.
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