Abstract
Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.
Highlights
Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS)
We have investigated the walnut population showing significant variations in terms of leaf budburst and flowering-related traits located in the Kahramanmaraş province, which is one of the walnut growing areas in Turkey, to (1) understand the genetic diversity and structure of walnut population and study its linkage disequilibrium, and (2) identify associations between molecular markers with time of leaf budburst and flowering-related traits using genome-wide association mapping to aid marker-assisted breeding in walnut
Because of the stringency of Bonferroni test that ignores linkage disequilibrium and assumes independent markers, we reported all Diversity Arrays Technology (DArT)-seq markers with p < 10−4 as suggestive associations if they had high linkage disequilibrium with a highly significant marker associated with a multi-trait quantitative trait loci (QTL)
Summary
Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs. The development of high-density DNA markers has played an important role in understanding the genetic diversity of different germplasm and in accelerating breeding programs and selection efficiency for complex traits in plants. This technology has developed a GBS platform known as DArT-seq, which provides an opportunity to select genome fractions corresponding predominantly to active genes. DArTseq offers affordable genome profiling by producing high-density SNPs as well as markers of presence and absence[19]
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