High-resolution association mapping with libraries of immortalized lines from ancestral landraces

Abstract

Key message Association mapping with immortalized lines of landraces offers several advantages including a high mapping resolution, as demonstrated here in maize by identifying the causal variants underlying QTL for oil content and the metabolite allantoin. Abstract Landraces are traditional varieties of crops that present a valuable yet largely untapped reservoir of genetic variation to meet future challenges of agriculture. Here, we performed association mapping in a panel comprising 358 immortalized maize lines from six European Flint landraces. Linkage disequilibrium decayed much faster in the landraces than in the elite lines included for comparison, permitting a high mapping resolution. We demonstrate this by fine-mapping a quantitative trait locus (QTL) for oil content down to the phenylalanine insertion F469 in DGAT1-2 as the causal variant. For the metabolite allantoin, related to abiotic stress response, we identified promoter polymorphisms and differential expression of an allantoinase as putative cause of variation. Our results demonstrate the power of this approach to dissect QTL potentially down to the causal variants, toward the utilization of natural or engineered alleles in breeding. Moreover, we provide guidelines for studies using ancestral landraces for crop genetic research and breeding.

Unraveling the potential of phenomic selection within and among diverse breeding material of maize (Zea mays L.)

“…The genotypes of the landraces group were immortalized as doubled-haploid lines and are comprised of the following 6 landraces: Campan-Galade (CG; n = 11) originating from France, Gelber Badischer (GB; n = 33) from Germany, Sankt Galler Rheintaler (RT; n = 14) from Switzerland, Satu Mare (SM; n = 53) from Romania, Strenzfelder (SF; n = 30) from Germany, and Walliser (WA; n = 59) from Switzerland. The plant material has been described in previous studies ( Böhm et al 2017 ; Würschum et al 2021 ). Three different location-year-combinations served as environments for the phenotypic data used in this study, the experimental station for plant breeding in Hohenheim (HOH; 48°43′05.7″N, 9°11′20.8″E; 389 m above sea level) during the field seasons 2019 and 2020 and the experimental station Eckartsweier (EWE; 48°32′24.7″N, 7°51′15.1″E; 139 m above sea level) during the field season 2020.…”

Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.)

“…These results are within the range of the polymorphism percent of 16. 90 To cross verify any discrepancies in the grouping of markers a plot of recombination fractions and LOD score between all the pairs of markers was developed (Supplementary Fig. 2), these analyses indicate the absence of linkage between the SNPs belonging to different linkage groups inferring correct grouping of markers.…”

How can we breed for phosphate efficiency in maize (Zea mays)?

“…In this study, we used 400 maize ( Zea mays L.) genotypes that have been described in detail previously (Weiß et al, 2022; Würschum et al, 2022). In brief, the investigated germplasm consisted of 200 elite lines (100 elite Flints [EF] and 100 elite Dents [ED]) and 200 European doubled haploid lines from landraces (11 individuals from Campan‐Galade [CG], 33 from Gelber Badischer [GB], 14 from Sankt Galler Rheintaler [RT], 30 from Strenzfelder [SF], 53 from Satu Mare [SM] and 59 from Walliser [WA]).…”