Large scale genome-wide association analysis identified QTLs associated with aluminum tolerance in chickpea

Chickpea has become an increasingly popular healthy food worldwide. Aluminum (Al) toxicity is a major hurdle for chickpea cultivation and yield improvement in acidic soils. However, the genetic mechanism of Al-tolerance in chickpea remains poorly understood. Here, we performed a large-scale hydroponics screening and SNP chip array genotyping of 1154 diverse chickpea accessions. Root lengths after 6 days cultivation under hydroponics in control (T0: pH 4.2) and Al treatment (T1: pH4.2, 15/20 μM Al³⁺) were measured. Root tolerance index (RTI = T1/T0) ranking revealed significant variations in chickpea Al-tolerance, with common Australian chickpea cultivars positioned in the low to medium range. Genome-wide association analyses revealed eight QTLs on chromosomes ca1 (CaAlt1-1), ca3 (CaAlt3-1), ca4 (CaAlt4-1, CaAlt4-2), ca5(CaAlt5-1), ca6 (CaAlt6-1), and ca7 (CaAlt7-1, CaAlt7-2) associated with T1, implying a multigenic genetic basis for Al-tolerance in chickpea. Specifically, CaAlt7-2 was associated with both T1 and RTI, whilst CaAlt4-2 was detected for T1 uniquely in the HatTrick x CudiB22C population. Al- tolerant and sensitive haplotypes for the identified QTLs were also identified. Organic acid transporter genes CaMATE2, CaMATE4, and CaALMT1 were found in proximal genomic regions to CaAlt7-2, CaAlt4-1, and CaAlt6-1, respectively. Further qRT-PCR in parental chickpea lines (HatTrick, Slasher, Gunas, CudiB) confirmed that CaMATE2 and CaMATE4 were strongly induced upon Al treatment. Interestingly, CaMATE2 was preferentially expressed in the upper part of the root, whilst CaMATE4 preferentially in the root tips, implying a potential complementary role in Al resistance. Their direct roles in Al tolerance and the potential alternative candidate genes near the QTLs require further investigation. This first report of QTLs on Al-tolerance in chickpea has substantially advanced our understanding of the genetic basis of Al tolerance in chickpea and will facilitate the rapid breeding of Al-tolerant chickpea cultivars for previously un-accessible acidic soils.