Abstract
ContextYield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces.ResultsUsing a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits.ConclusionsOur phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice.
Highlights
Rice (Oryza sativa L.) is one of the most important food crops for more than half of the world’s population and is considered as a model species for grasses for important agronomic traits
Phenotypic analysis Phenotyping for genome-wide association study (GWAS) analysis was performed in field conditions near Hanoi at the Plant Resource Center located at An Khanh, Hoai Duc (21° 00′ 01′′ N and 105° 72′ 55′′ E) and Van Giang Agricultural Station located at Van Giang, Hung Yen (20° 90′ 42“N and 105° 94’ 78” E) during the wet season of 2014 and 2015, respectively
Calculation of heritability scores showed that the scores of almost all panicle traits were similar and with high values (H2 > 0.85) for the two years, except for tertiary branch number (TBN) which showed the lowest heritability score (0.21 in 2014 and 0.43 in 2015) and the highest variation with a coefficient of variation (CV) of the trait of over 35% with no significant genotypic effect (Table 1)
Summary
Rice (Oryza sativa L.) is one of the most important food crops for more than half of the world’s population and is considered as a model species for grasses for important agronomic traits. Quantitative trait locus (QTL) mapping using bi-parental populations of O. sativa has allowed the identification of QTLs related to characters such as panicle branching or size (e.g. Gn1a, DEP1, IPA1/WFP), grain weight or size (e.g. GS3, GW2, qSW5/GW5) and grain filling (e.g. GIF1), revealing a large number of genes governing yield components [1,2,3]. The identification of other QTLs has shown that yield potential can be influenced indirectly by factors relating to the physiological state of the plant. Some specific alleles of the genes corresponding to these yield-related QTLs were selected during domestication and/or breeding programs for high yields
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