Abstract
Potassium use efficiency, a complex trait, directly impacts the yield potential of crop plants. Low potassium efficiency leads to a high use of fertilizers, which is not only farmer unfriendly but also deteriorates the environment. Genome-wide association studies (GWAS) are widely used to dissect complex traits. However, most studies use single-locus one-dimensional GWAS models which do not provide true information about complex traits that are controlled by multiple loci. Here, both single-locus GWAS (MLM) and multi-locus GWAS (pLARmEB, FASTmrMLM, mrMLM, FASTmrEMMA) models were used with genotyping from 90 K Infinium SNP array and phenotype derived from four normal and potassium-stress environments, which identified 534 significant marker-trait associations (MTA) for agronomic and potassium related traits: pLARmEB = 279, FASTmrMLM = 213, mrMLM = 35, MLM = 6, FASTmrEMMA = 1. Further screening of these MTA led to the detection of eleven stable loci: q1A, q1D, q2B-1, q2B-2, q2D, q4D, q5B-1, q5B-2, q5B-3, q6D, and q7A. Moreover, Meta-QTL (MQTL) analysis of four independent QTL studies for potassium deficiency in bread wheat located 16 MQTL on 13 chromosomes. One locus identified in this study (q5B-1) colocalized with an MQTL (MQTL_11), while the other ten loci were novel associations. Gene ontology of these loci identified 20 putative candidate genes encoding functional proteins involved in key pathways related to stress tolerance, sugar metabolism, and nutrient transport. These findings provide potential targets for breeding potassium stress resistant wheat cultivars and advocate the advantages of multi-locus GWAS models for studying complex traits.
Highlights
Potassium (K) plays a critical role in plant growth and development, elucidated by its multidimensional capacity of regulating the plant physiological systems such as enzymes activation, membrane potential, osmoregulation, photosynthesis, and osmotic balance (Clarkson and Hanson, 1980; Pettigrew, 2008; Wang and Wu, 2017)
The panel was categorized into four groups on the basis of release time of cultivars: group-I consisted of 20 varieties of pre-green revolution release (1965 or earlier), groupII consisted of 30 varieties of green revolution release (19651979), while group-III and group-IV each had 50 cultivars comprised of post-green revolution release and elite cultivars, respectively (Table S1)
Most of the complex traits like K-use efficiency (KUE) are dominated by major genes, the one-dimensional model can not detect associations with the variation of polygenes due to the limitations of the model (Lü et al, 2018)
Summary
Potassium (K) plays a critical role in plant growth and development, elucidated by its multidimensional capacity of regulating the plant physiological systems such as enzymes activation, membrane potential, osmoregulation, photosynthesis, and osmotic balance (Clarkson and Hanson, 1980; Pettigrew, 2008; Wang and Wu, 2017). As for K, different plant species or even the different genotypes of the same species are known to have a varied K-uptake and utilization efficiency (Pettersson and Jensen, 1983; Guoping et al, 1999) This provides a possibility for the genetic dissection of crop KUE (Wang and Wu, 2015). Several studies in the past have reported the genotypic variation of KUE in wheat (Guoping et al, 1999; George et al, 2002; Damon and Rengel, 2007; Pettigrew, 2008; Rengel and Damon, 2008; Wang and Wu, 2015) This suggests that the genetic improvement of crops can be carried out by selecting important quantitative trait loci (QTL) associated to KUE. This approach of identifying MQTL by meta-analysis was first proposed by Goffinet and Gerber (2000), and has since been applied in many crops including wheat (Griffiths et al, 2009; Gegas et al, 2010; Quraishi et al, 2017)
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