Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice

Niña Gracel B Dimaano,Aurora M Baltazar,Maria Genaleen Q Diaz,Bart L Acero,Zhikang Li,Yun Long Pang,Pompe C Sta Cruz,Anumalla Mahender,Jauhar Ali

doi:10.1007/s10681-020-02694-8

Abstract

Weed competitive ability (WCA) is vital for the improvement of grain yield under direct-seeded and aerobic rice ecosystems where weeds are a major limiting factor. Early seed germination (ESG) and early seedling vigor (ESV) are the crucial traits for WCA. This study attempted to map the quantitative trait loci (QTLs) and hotspot regions governing ESG and ESV traits. A total of 167 BC1F5 selective introgression lines developed from an early backcross population involving Weed Tolerant Rice 1 (WTR-1) as the recipient parent and Y-134 as the donor parent were phenotyped for ESG and ESV traits. Analysis of variance revealed significant differences in ESG-related traits except for root length and in ESV-related traits except for plant height at 7 days after sowing. A total of 677-high quality single nucleotide polymorphism (SNP) markers were used to analyze the marker-trait association from a 6 K SNP genotyping array. Forty-three QTLs were identified on all chromosomes, except on chromosomes 4 and 8. Thirty QTLs were contributed by a desirable allele from Y-134, whereas 13 QTLs were from WTR-1. Twenty-eight of the identified genetic loci associated with ESG and ESV traits were novel. Two QTL hotspot regions were mapped on chromosomes 11 and 12. The genomic regions of QTL hotspots were fine-tuned and a total of 13 putative candidate genes were discovered on chromosomes 11 and 12 collectively. The mapped QTLs will be useful in advancing the marker aided-selection schemes and breeding programs for the development of rice cultivars with WCA traits.

Highlights

IntroductionBy 2050, 42% more rice yield will be needed to meet the rapidly growing global demand (Ray et al 2013)
Rice is a major food crop for half of the world’s population
Among the ten Early seed germination (ESG) traits, the highest coefficients of variation (CV) values were identified in average fresh weight (AFW) (48.25%) and 1st germination count (GC) after 48 h (44.05%), whereas the lowest CV was observed in total dry weight of germinated seeds (TDGS) (17.83%) and shoot length (SL) (18.58%)

Summary

Introduction

By 2050, 42% more rice yield will be needed to meet the rapidly growing global demand (Ray et al 2013). The future threat to natural resources, rising labor shortages, declining arable lands, increasing prices of fertilizer and pesticide inputs, energy scarcity, and changing climatic conditions are the major factors contributing to the decrease in rice production (Singh et al 2013). To overcome these constraints, shifting from the conventional puddled transplanted rice system to direct-seeded rice (DSR) is the most promising strategy (Chauhan and Abugho 2013; Mahender et al 2015). The vigorous growth of weeds is one of the major biological constraints to attain optimal grain yield in the DSR system (Chauhan et al 2015)

Methods

Results

Discussion

Conclusion