Abstract
The number of grains per panicle is an important yield-related trait in cereals which depends in part on panicle branching complexity. One component of this complexity is the number of secondary branches per panicle. Previously, a GWAS site associated with secondary branch and spikelet numbers per panicle in rice was identified. Here we combined gene capture, bi-parental genetic population analysis, expression profiling and transgenic approaches in order to investigate the functional significance of a cluster of 6 ANK and ANK-TPR genes within the QTL. Four of the ANK and ANK-TPR genes present a differential expression associated with panicle secondary branch number in contrasted accessions. These differential expression patterns correlate in the different alleles of these genes with specific deletions of potential cis-regulatory sequences in their promoters. Two of these genes were confirmed through functional analysis as playing a role in the control of panicle architecture. Our findings indicate that secondary branching diversity in the rice panicle is governed in part by differentially expressed genes within this cluster encoding ANK and ANK-TPR domain proteins that may act as positive or negative regulators of panicle meristem's identity transition from indeterminate to determinate state.
Highlights
Rice yield is determined by several traits, including the number of grains carried on each panicle [1,2]
A new QTL with co-location of spikelet number (SpN) and secondary branch number (SBN) traits was identified by genome-wide association study in a Vietnamese rice landrace panel
A set of four Ankyrin and Tetratricopeptide repeat domain-encoding genes was identified from this QTL based on their difference of expression levels between two contrasted haplotypes for the SpN and SBN traits
Summary
Rice yield is determined by several traits, including the number of grains carried on each panicle [1,2] This in turn is dependent on the architecture of the panicle, which consists of a series of axes of different successive orders: rachis; primary branches; secondary branches; potentially tertiary branches; and spikelets. Since the rice spikelet typically contains a single fertile floret, the number of spikelets usually determines in fine the number of grains that can be produced per panicle. In this context, genetic selection of panicle branching traits to improve yield potential is of great importance in breeding programmes. Various genes that control these two processes governing panicle architecture were identified through the characterization of mutants and QTLs, shedding light on the signalling pathways and protein interactions involved [1,2,3,4,5]
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