Advancing understanding of the genetic basis of grain protein content in wheat through hyperspectral imaging and genomicsTools Safdar, Luqman (2025) Advancing understanding of the genetic basis of grain protein content in wheat through hyperspectral imaging and genomics. PhD thesis, University of Nottingham.
AbstractGrain protein content (GPC) determines the rheological properties of bread wheat and is a vital nutritional trait because wheat accounts for ~20% of global caloric and protein intake. The genetic basis of GPC is historically associated with senescence and post-anthesis nitrogen (N) remobilisation from source to sink tissues through Gpc-B1 alleles. Recent research has suggested that vascular architecture can also affect GPC variation through the activity of a HOMOEOBOX DOMAIN-2 (HB-2) gene. My thesis comprehensively investigated the physiological and biological mechanisms underpinning GPC and N remobilisation in wheat lines that contain variant HB-2 alleles. I investigated the newly identified HB-2 alleles for their effect on grain yield and N-use efficiency in the spring wheat Cadenza background using glasshouse experiments. These experiments showed that HB-2 improved GPC without a yield trade-off, particularly in response to N limitation, which is attributable to enhanced sink strength facilitated by higher HB-2 expression during the early stages of inflorescence development. Analyses of the grain transcriptome in these lines under two levels of N suggested that protein storage-related processes respond to N availability difference during early- to mid-filling. Moreover, a positive correlation was detected between co-upregulated gene networks and GPC at the early-filling stage. Notably, the grain transcriptome of HB-2 mutants grown under limited N responded similarly to wild-type supplied with optimum N, indicating HB-2 could be a promising candidate for improving N-use efficiency of wheat; results shown here support further investigation of HB-2 alleles in backgrounds of elite cultivars and different environments. To complement my analysis of the HB-2 alleles, I investigated the A. E. Watkins global wheat landrace collection to identify novel genetic factors associated with GPC that may have been lost during modern breeding. I developed a single grain-based protein prediction model using hyperspectral imaging and machine learning. I analysed single wheat grains from two field trials in the UK at different sites/years. The single grains were phenotyped for GPC, GPC heterogeneity (the variation among single grains within a genotype), grain weight, and grain morphological features such as length, width and area. These phenotypes were associated with genetic variation in the Watkins panel using ~90 million single nucleotide polymorphisms through genome-wide association analyses. This work identified promising loci on chromosomes 6A, 6D and 7D of the Watkins landraces that showed significant association with GPC. These loci may present an opportunity to incorporate novel GPC-associated genetic variation into modern wheat varieties. Moreover, my results showed that GPC heterogeneity is a heritable trait with a stable locus at chromosome 6A contributing ~17% of the 25% heritable variance. My thesis provides genetic insights for improving GPC in wheat without compromising yield, including the identification of molecular processes that are associated with higher protein content. It also provides valuable technical advances for screening large populations that will help breeding programs accelerate the evaluation of GPC while identifying the importance of poorly understood traits such as grain protein heterogeneity.
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