Detection of genomic regions associated with tiller number in Iranian bread wheat under different water regimes using genome-wide association study

Sayedeh Saba Bilgrami,Khadijeh Razavi,Hadi Darzi Ramandi,Barat Ali Fakheri,Elahe Tavakol,Mostafa Ghaderian,Vahid Shariati,Nafiseh Mahdi Nezhad

doi:10.1038/s41598-020-69442-9

Abstract

Two of the important traits for wheat yield are tiller and fertile tiller number, both of which have been thought to increase cereal yield in favorable and unfavorable environments. A total of 6,349 single nucleotide polymorphism (SNP) markers from the 15 K wheat Infinium array were employed for genome-wide association study (GWAS) of tillering number traits, generating a physical distance of 14,041.6 Mb based on the IWGSC wheat genome sequence. GWAS analysis using Fixed and random model Circulating Probability Unification (FarmCPU) identified a total of 47 significant marker-trait associations (MTAs) for total tiller number (TTN) and fertile tiller number (FTN) in Iranian bread wheat under different water regimes. After applying a 5% false discovery rate (FDR) threshold, a total of 13 and 11 MTAs distributed on 10 chromosomes were found to be significantly associated with TTN and FTN, respectively. Linked single nucleotide polymorphisms for IWB39005 (2A) and IWB44377 (7A) were highly significantly associated (FDR < 0.01) with TTN and FTN traits. Moreover, to validate GWAS results, meta-analysis was performed and 30 meta-QTL regions were identified on 11 chromosomes. The integration of GWAS and meta-QTLs revealed that tillering trait in wheat is a complex trait which is conditioned by the combined effects of minor changes in multiple genes. The information provided by this study can enrich the currently available candidate genes and genetic resources pools, offering evidence for subsequent analysis of genetic adaptation of wheat to different climatic conditions of Iran and other countries.

Highlights

Two of the important traits for wheat yield are tiller and fertile tiller number, both of which have been thought to increase cereal yield in favorable and unfavorable environments
Heritability of 48 and 43% was estimated for total tiller number (TTN) and fertile tiller number (FTN), respectively, under all conditions (Supplementary Table S2)
These MQTLs with relatively narrow confidence interval (CI) had the highest number of quantitative trait loci (QTL) for TTN and FTN traits and considered as one of the most reliable chromosomal positions that can assist wheat molecular breeding. These results suggest that some marker-trait associations (MTAs) identified in our study can serve as important MTAs for marker-assisted selection and gene cloning of important tiilering genes

Summary

Introduction

Two of the important traits for wheat yield are tiller and fertile tiller number, both of which have been thought to increase cereal yield in favorable and unfavorable environments. QTL mapping and genome-wide association studies (GWAS) have become two key approaches to understanding the genetic bases and dissection of complex genes and controlling important features such as tillering traits. In addition to the benefits of GWAS to QTL mapping, the meta-analysis as a statistical technique was developed to combine consensus loci from many individual QTL studies for any number of traits into a single dataset to identify most likely position and confidence interval (CI) of QTL r egions[10] This method has been used to determine consensus regions of the genome across multiple QTL studies for their effects and consistency across different genetic backgrounds and environments, to refine and confirm QTL positions on a consensus map via mathematical models. A number of studies have applied the QTL meta-analysis method to different traits in wheat, including root morphological traits[13,16], grain traits[11], fusarium head blight resistance[14,17], adaptation to drought and heat stress[18] and leaf rust resistance[19]

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Discussion

Conclusion