Fine mapping coincident QTL on a chromosome 6H introgression region from unadapted germplasm into elite malting barley

Abstract

Breeders strive to improve a cultivar for multiple traits. This can be challenging when these traits are unfavorably associated. This study fine maps several traits associated with the centromeric region of chromosome 6H by mendelizing the region using near-isogenic lines (NILs). A NIL carrying an introgression from the landrace Chevron for this region was crossed to a malting cultivar Lacey to create 1941 F2 individuals from which recombinant NILs (rNILs) for the introgressed region were developed. We developed a dense genetic map using 249 F4-derived rNILs and phenotyped 101 of them in field and greenhouse trials for fourteen traits. We observed transgressive segregation for Fusarium head blight (FHB) severity, grain protein concentration (GPC), days to senescence, normalized difference vegetation index (NDVI), seedling net blotch, and heading date. We detected QTL for eleven traits. For ten of the traits, we detected multiple QTL with opposite allelic effects for each of them. Six traits that showed transgressive segregation mapped to multiple QTL with opposite allelic effects. QTL for deoxynivalenol (DON) accumulation mapped to separate regions to that for GPC and FHB severity, suggesting DON accumulation was likely associated through linkage rather than pleiotropy to GPC and FHB severity. While there was no recombinant line possessing all favorable alleles in this region, we identified two rNILs with numerically lower FHB severity and DON accumulation and GPC similar to Lacey. Seven traits (NDVI, days to senescence, percent stem breakage, GPC, heading date, adult net blotch severity and seedling net blotch severity) mapped to a single region, close to the physical location of the NAM-1/Gpc-1 gene. This gene is known to encode a NAC transcription factor that might be involved in nitrogen remobilization from leaves to grains during senescence. Findings in this study about coincident QTL controlling days to senescence, NDVI, percent stem breakage, and GPC might aid in the understanding of nitrogen remobilization process. Our fine mapping study revealed a complex genetic architecture for eleven traits associated with this chromosome 6H region and highlights the need for recombination to uncouple unfavorable linkages in breeding programs.