Combining Image Analysis, Genome Wide Association Studies and Different Field Trials to Reveal Stable Genetic Regions Related to Panicle Architecture and the Number of Spikelets per Panicle in Rice

Maria C Rebolledo,Cecile Grenier,Alexandra L Peña,Michael Dingkuhn,Joe Tohme,Daniel F Cruz,Jorge Duitama

doi:10.3389/fpls.2016.01384

Maria C Rebolledo, Cecile Grenier + Show 5 more

Open Access

https://doi.org/10.3389/fpls.2016.01384

Copy DOI

Abstract

Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs. Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN, and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN), suggesting independent genetic control. Twenty- three GWAS sites were detected with P ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E−04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported. The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding.

Highlights

Growing world population and the effects of global climate change are increasing the demand for higher crop yields
Despite some existing knowledge on the genetic control of the number of spikelets per panicle, there is little evidence on the added value for breeding of secondary traits, such as panicle architecture traits. This may be explained by the lack of undestanding of (i) the role of each panicle architecture component trait and their mutual compensations, (ii) the genetic architecture of panicle component traits, and (iii) the stability of the panicle component traits across contrasting environmental conditions
It was expected that the phenotyping of panicle architecture traits would provide further insight into trait-trait correlations and trade-offs defining the total number of spikelets per panicle, while the analysis of two contrasting conditions would provide insights into environmental and genetic control

Summary

Introduction

Growing world population and the effects of global climate change are increasing the demand for higher crop yields. New rice varieties with high yield potential have been a major target of crop improvement in rice (Peng et al, 1999). In Asia and Africa farmers are considering shifting to DRS (Farooq et al, 2011), varieties currently used for DRS were bred for transplanted culture in puddle soils. Under both production systems increasing sink size at flowering is a priority trait to increase yield potential in rice (Dingkuhn et al, 1991, 2015; Foulkes et al, 2011). The genetic improvement of the number of spikelets per panicle may benefit from its dissection into component traits of lesser genetic complexity, such as panicle architecture traits (AL-Tam et al, 2013; Crowell et al, 2014)

Objectives

Methods

Results

Conclusion