Location: Small Grain and Food Crops Quality Research
Project Number: 3060-21650-002-021-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2021
End Date: Dec 31, 2025
Objective:
(1) Introduce genes into key U.S. chickpea cultivars by marker-assisted backcrossing for drought-tolerant yield from a cultivated chickpea; (2) Introduce genes into key U.S. chickpea cultivars by marker-assisted backcrossing for high temperature pod setting from a recently found wild chickpea; (3) Evaluate introgressed material from Objectives 1 and 2 under stress and non-stress conditions to identify top performing selections; and (4) Develop functional molecular markers for further marker-assisted breeding into U.S. cultivars.
Approach:
The U.S. elite cultivars ‘Nash’, ‘BillyBeans’ and ‘UC27’ were selected to represent the major market types (kabuli export, processing, canning respectively) and chickpea cultivation areas (Northern Plains, Pacific Northwest area, inland California respectively) and will be used as recurrent (elite) parents for introgression breeding. Due to the current lack of molecular markers for the U.S. elite material, F2 plants from these crosses have been selected with a morphological marker (purple flowers) that is loosely linked to the chromosome 4 drought tolerance Quantitative Trait Locus (QTL) of ICC4958 for ongoing backcrossing in summer 2021. For subsequent cycles of backcrossing, markers developed from Objective 4 will be used for marker assisted selection (MAS) to screen backcross individuals to select those harboring the ICC4958 chr4 haplotype as heterozygotes among BCnF1s and homozygotes in F2/3 progenies for phenotyping (Objective 3). For heat tolerance introgression, Kalkan F5s (identified in the 2017/8 field heat screen) will be grown with an elevated reproductive phase temperature (daytime high 35C and night low of 20C at/after flowering) in a greenhouse. The most heat tolerant (highest podding) individual F5 plants will be chosen for use in greenhouse crossing to the three U.S. elite cultivars. F1 hybrids obtained will be greenhouse grown, selfed, and F2 seed harvested. 300 greenhouse-grown F2 plants (100/elite parent) will be sampled for leaf tissue for use in heat tolerance QTL mapping/ marker development. For Objective 4, molecular markers for use in marker assisted backcrossing will be identified by using whole genome sequencing of the three US elite cultivars. The resulting Single Nucleotide Polymorphism (SNP) variant calls of US cultivars against ICC4958 will be filtered for SNPs at the chr4 QTL hotspot and 8-12 SNPs selected for conversion to KASP genotyping assays for use in marker assisted selection for the drought QTL. To identify markers for heat tolerance QTLs from the Kalkan donor, RADseq reduced representation sequencing will be done on the F2 introgression populations (3 x 100 F2s). To identify SNPs, RADseq data will be aligned to the whole genome data of the U.S. cultivars generated in Year 1. SNPs with data in >80% of each F2 population and intermediate frequencies will be selected for QTL mapping with phenotypic data. The top 1-2 QTLs will be prioritized for marker development using SNPs in QTL flanking regions for KASP marker development.
