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. 2020;216(10):159.
doi: 10.1007/s10681-020-02694-8. Epub 2020 Sep 19.

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

Niña Gracel B Dimaano #  1 , Jauhar Ali #  2 , Anumalla Mahender #  2 , Pompe C Sta Cruz  1 , Aurora M Baltazar  1 , Maria Genaleen Q Diaz  1 , Yun Long Pang  3 , Bart L Acero Jr  2 , Zhikang Li  4
Affiliations

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

Niña Gracel B Dimaano et al. Euphytica. 2020.

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.

Keywords: Early seed germination; Early seedling vigor; Quantitative trait loci; Selective introgression lines; Single nucleotide polymorphism; Weed competitive ability.

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Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Distribution of the polymorphic single nucleotide polymorphisms (SNPs) and gaps between the two adjacent markers in all chromosomes
Fig. 2
Fig. 2
Phenogram plot showing the forty-three quantitative trait loci (QTLs) for early seed germination (ESG) and early seedling vigor (ESV) related traits in rice. The twelve chromosomes were displayed with blue color lines indicating the distribution of polymorphic single nucleotide polymorphisms (SNPs) according to the physical map. On the left side of the chromosomes were small segments of colored vertical bars representing the previously identified germination and seedling vigor QTLs that co-localized with the QTLs identified in this study. ESG QTLs previously identified were qGR5-1 (Miura et al. 2001), qPH11.2 (Sandhu et al. 2014), qSV11c (Chen et al. 2019), qLTG-11 (Saito et al. 2001), qSV12b (Chen et al. 2019), and qAG12 (Septiningsih et al. 2013). ESV QTLs previously identified were qSV1c (Chen et al. 2019), qGR-138 (Wang et al. 2010), qSV3a (Chen et al. 2019), qGR2 (Diwan et al. 2013), qSEV-2-2 (Lu et al. 2007), qSDW2 (Han et al. 2007), and qCD-9-3 and qCV-9 (Yang et al. 2019)
Fig. 3
Fig. 3
QTLs strong effects of early seed germination (ESG) and early seedling vigor (ESV) traits (LOD > 3.0) identified in the early backcross generation of selective introgression lines (SILs). The plots A and B represent the additive effect and allele effect of the 29 QTLs in ESG and 15 QTLs in ESV QTLs
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