Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice

• Published in: BMC genomics Vol. 21; no. 1; p. 294
• Main Authors: Khahani, Bahman, Tavakol, Elahe, Shariati, Vahid, Fornara, Fabio
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 10.04.2020; BioMed Central; BMC
• Subjects: Barley; Breeding; Cereals; Chromosome Mapping - methods; Chromosomes; Chromosomes, Plant - genetics; Comparative analysis; Confidence intervals; Crop yield; Crop yields; Edible Grain - genetics; Edible Grain - growth & development; Genes; Genetic Linkage; Genetic markers; Genome-Wide Association Study - methods; Genomes; Genomics; Hordeum - genetics; Hordeum - growth & development; Markers; MQTLs; Oryza - genetics; Oryza - growth & development; Phenotype; Plant Breeding; Plant Proteins - genetics; Population genetics; Populations; Quantitative genetics; Quantitative Trait Loci; Quantitative Trait, Heritable; Rice; Studies; Synteny; Synteny analysis; yield-components; Zea mays - genetics; Zea mays - growth & development; yield-components; Synteny analysis; MQTLs; Breeding
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6702-1

Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development. A comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits. This comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.