QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems.

Ricky Vinarao,Christopher Proud,Shu Fukai,Peter Snell,Jaquie Mitchell

doi:10.3390/plants10102099

Abstract

Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3–17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7–15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4’s effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.

Highlights

To feed the increasing number of rice consumers by 2030, world rice production has to increase by 40% [1]
This study validated the effect of qRCA4 in multiple genetic backgrounds further reinforcing its value in improvement of rice genotypes for Aerobic rice production (AP) adaptation
High-throughput kompetitive allele specific PCR (KASP) single nucleotide polymorphism (SNP) molecular markers were developed to tag this genomic region which will facilitate its seamless introgression into target recipient genotypes especially in breeding programs where AP adaptation traits are important

Summary

Introduction

To feed the increasing number of rice consumers by 2030, world rice production has to increase by 40% [1]. This is a tall order considering the devastating negative effects of climate change such as looming water crisis brought about by climate change, increasing population, and higher food demand [2]. Water availability in AP system is generally high, transient water deficit may develop between irrigation events. This is distinct from water deficit as commonly perceived in relatively low yielding upland cultivation

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Results

Conclusion