Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

Abstract

Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower (Brassica oleracea var. botrytis) by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS) and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding.

Cauliflower Growth, Yield and Quality Response to Nitrogen Fertilization and Micronutrients Foliar Application in Newly Reclaimed Areas

“…Contrary, Singh et al (2017) reported that soil application of Borax (20 kg/ha) combined with Sodium molybdate (2 kg/ha) as sources of B and Mo, respectively, accelerated the early mature yield of cauliflower. However, insignificant effects of nitrogen, micronutrient application and their interaction on number of days to maturity might be due to its high heritability, whereas, it was reported that number of days to budding is a highly heritable trait (86 and 94%), which indicates that this trait is stable and not strongly affected by environmental factors (Yousef et al, 2015;Thorwarth et al, 2018).…”

Identification of QTLs associated with curd architecture in cauliflower

“…For example, the specific curd phenotype is revealed to be governed by BoCAL gene [2,3], BoAP1 gene determines the divergence between cauliflower curd and broccoli head phenotypes [4,5], while the Or Gene encoding a plastid associated protein results in an orange curd that is rich in β-carotene [6]. Recently, a genome wide association study based on 174 randomly selected cauliflower gene bank accessions identified a total of 24 significant associations for curd-related traits [7].…”

Evolutionary and ecological functional genomics, from lab to the wild

“…() showcased the method's power for mapping natural genetic variants for more than 100 traits in A. thaliana . To date, GWAS have also identified the genetic basis of numerous agronomic traits, speeding up breeding programs of crops such as maize (Jiao et al ., ; Zila et al ., ; Wallace et al ., ; Hu et al ., ; Xu et al ., ) and rice (Huang et al ., , ; McCouch et al ., ; Wang et al ., ; Wang et al ., ), as well as crops with less well‐developed molecular resources such as wheat (Liu et al ., ; Kristensen et al ., ), soybean (Fang et al ., ), barley (Sharma et al ., ), cotton (Fang et al ., ; Du et al ., ), cassava (Kayondo et al ., ), foxtail millet (Jia et al ., ), spinach (Ma et al ., ) and cauliflower (Thorwarth et al ., ). GWAS are a particularly relevant tool for perennial species such as apple (Urrestarazu et al ., ), citrus (Minamikawa et al ., ), eucalyptus (Resende et al ., ) and poplar (Liu et al ., ).…”