Exploiting sorghum genetic diversity for enhanced aluminum tolerance: Allele mining based on the AltSB locus

Abstract

Root damage due to aluminum (Al) toxicity restricts crop production on acidic soils, which are extensive in the tropics. The sorghum root Al-activated citrate transporter, SbMATE, underlies the Al tolerance locus, AltSB, and increases grain yield under Al toxicity. Here, AltSB loci associated with Al tolerance were converted into Amplification Refractory Mutation System (ARMS) markers, which are cost effective and easy to use. A DNA pooling strategy allowed us to identify accessions harboring rare favorable AltSB alleles in three germplasm sets while greatly reducing genotyping needs. Population structure analysis revealed that favorable AltSB alleles are predominantly found in subpopulations enriched with guinea sorghums, supporting a possible Western African origin of AltSB. The efficiency of allele mining in recovering Al tolerance accessions was the highest in the largest and highly diverse germplasm set, with a 10-fold reduction in the number of accessions that would need to be phenotyped in the absence of marker information. Finally, Al tolerant accessions were found to rely on SbMATE to exclude Al3+ from sensitive sites in the root apex. This study emphasizes gene-specific markers as important tools for efficiently mining useful rare alleles in diverse germplasm, bridging genetic resource conservation efforts and pre-breeding for Al tolerance.

Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population

“…For example, in sorghum, Alencar Figueiredo et al (2008) reported on remarkably variable withingene LD, encompassing whole genes (> 4 Kb) for Opaque2, intensive intragenic recombination happening within only 244 bp in Waxy, and very weak LD along Brittle2. Lack of salient associations of GBS-SNPs near SbMATE with Al tolerance is influenced by the need for population structure cofactors in the association model, the low frequency of Al tolerance and low LD in the SbMATE region, which was found to persist to up to around 500 bp, resulting in intragenic recombination and great haplotype diversity for the Al tolerance gene (Caniato et al 2014;Hufnagel et al 2018). Because rare alleles are not efficiently sampled by the skim sequencing of GBS using moderate population sizes, SbMATE-specific markers identified via a targeted associating mapping approach (Caniato et al 2014), rather than any GBS SNP marker, showed by far the highest association signals for Al tolerance in the diverse association panel used by Melo et al (2019).…”

Construction of an ultra-high-density consensus genetic map and analysis of recombination rate variation in Sorghum bicolor

“…High-density genetic or linkage maps are necessary to investigate the inheritance of qualitative and quantitative traits, design markers for molecular breeding, perform map-based gene cloning, and conduct comparative genomic investigations. Molecular breeding is more effective when densely-marked molecular map (Hufnagel et al 2018). The consensus genetic map increases the diversity and quality of markers and the frequency of polymorphic markers at important chromosomal intervals.…”

Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact

“…This reverse genetic approach can find useful loss-of-function (LOF) variation that would not be found by phenotyping as its effect is hidden due to gene/ allele redundancy (Comai, 2005), particularly in polyploid or highly heterozygous material such as Urochloa, and provides the basis for perfect markers in crosses for following the alleles. Successful examples of allele mining for natural variation in known genes include studies on rice germplasm for starch synthesis genes (Butardo et al, 2017) and on Sorghum germplasm for a gene responsible for aluminium tolerance (Hufnagel et al, 2018).…”