Preprint Article Version 1 This version is not peer-reviewed

Novel Quantitative Trait Loci for Weed Competitive Ability Traits Using the Early Generation of Backcross Rice Populations

Version 1 : Received: 29 August 2018 / Approved: 29 August 2018 / Online: 29 August 2018 (10:46:02 CEST)

How to cite: Dimaano, N.; Ali, J.; Anumalla, M.; Cruz, P.; Baltazar, A.; Diaz, M.; Pang, Y.L.; Acero, B.; Li, Z. Novel Quantitative Trait Loci for Weed Competitive Ability Traits Using the Early Generation of Backcross Rice Populations. Preprints 2018, 2018080493 (doi: 10.20944/preprints201808.0493.v1). Dimaano, N.; Ali, J.; Anumalla, M.; Cruz, P.; Baltazar, A.; Diaz, M.; Pang, Y.L.; Acero, B.; Li, Z. Novel Quantitative Trait Loci for Weed Competitive Ability Traits Using the Early Generation of Backcross Rice Populations. Preprints 2018, 2018080493 (doi: 10.20944/preprints201808.0493.v1).

Abstract

Weed competitive ability (WCA) is a desirable key trait for the improvement of grain yield under direct-seeded rice (DSR) and the aerobic rice ecosystem. The present study targeted screening of 167 introgression lines (ILs) of a Green Super Rice (GSR) IR2-6 population derived from a cross between Weed Tolerant Rice 1 (WTR1) as the recipient parent and Y134 as the donor parent developed at IRRI for weed competitiveness in screen house conditions (SHC). The ILs were phenotyped for WCA traits such as early seed germination (ESG) and early seedling vigor (ESV) in Petri dishes and pot experiment conditions. The results of phenotypic variance revealed ESG-related traits, especially first germination count (1st GC) that positively correlated with second germination count (2nd GC), germination percentage (GP), total dry weight (TDW), total fresh weight (TFW), and vigor index (VI-1), whereas, in ESV, all the traits were positively correlated with each other except for three traits: root dry weight (RDW), 1st GC, and GP-2. The ESG and ESV traits are vital for weed competitiveness. A 6K SNP array was used to study the genetic association for the WCA traits. Forty-four QTLs for WCA traits were mapped on all chromosomes (except on chromosomes 4 and 8) through single marker analysis (SMA). Out of 44 QTLs, 29 were associated with ESG traits and 15 with ESV traits, with LOD scores of 2.93 to 8.03 and 2.93 to 5.04 and explained phenotypic variance ranging from 7.85% to 19.9% and from 7.85% to 13.2%, respectively. However, 31 QTLs were contributed by a negative additive allele from Y134, whereas a positive additive allele was contributed by WTR1 in 13 QTLs. Among them, two QTL hotspot regions were mapped on chromosome 11 (24.7-27.9 Mb) and chromosome 12 (14.8-17.4 Mb). The majority of the QTLs related to WCA traits were grouped into two QTL hotspots: QTL hotspot-I (qAFW11.1, qFC11.1, qFC11.2, qSC11.1, qGP-111.1, qGP-111.2, qTFGS11.1, qVI-111.1, and qVI-111.2) and QTL hotspot-II (qFC12.1, qFC12.2, qSC12.1, qFC12.2, qGP-112.1, qGP-112.2, qTFGS12.1, qTFGS12.2, qVI-112.1, qIV12.2, qFC12.1, and qGC12.2), and a few of them were co-localized on chromosomes 11 and 12. Further, we fine-tuned in the genomic regions of QTL hotspots and identified a total of 13 putative candidate genes on chromosomes 11 and 12 collectively. The present study is the first report on the genetic basis of WCA-related traits and the co-localized QTLs, which could be highly valuable in future breeding programs aiming to improve WCA in rice.

Subject Areas

Weed competitive ability; early seed germination and seedling vigor traits; quantitative trait loci (QTLs); single nucleotide polymorphism; direct seeded rice

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