Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

Yang, Jing; Sun, Kai; Li, Dongxiu; Luo, Lixin; Liu, Yongzhu; Huang, Ming; Yang, Gangyi; Liu, Hong; Wang, Hui; Chen, Zhiqiang; Guo, Tao

doi:10.1186/s12864-019-5741-y

Cited by 55 publications

(44 citation statements)

References 49 publications

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“…Present findings revealed 38 putative QTLs for 6 traits on chromosomes 1,2,3,4,5,6,7 and 10. Several studies have been reported that usually QTL cluster responsible for correlated traits lie in the same genomic region confirming stable QTL (Gimhani et al 2016;Marathi et al 2012;Yang et al 2019). This QTLs cluster of different traits may be due to the presence of pleiotropy or Sabouri and Sabouri (2008), Zang et al (2008) tight linkage of genes controlling the traits (Gao et al 2013;Gimhani et al 2016).…”

Section: Discussionmentioning

confidence: 72%

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

Jahan

Zhang

et al. 2019

Plant Growth Regul

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Salinity is one of the major abiotic stresses limiting rice production worldwide. Understanding the genetic basis of salinity tolerance is key for rice breeding. In this study, a recombinant inbred line (RIL) population derived from a super hybrid rice Liang-You-Pei-Jiu (LYP9) parents 93-11 and PA64s, exhibited variation in phenotypes including shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW) under 50 and 100 mM NaCl stress. QTL analysis identified a total of 38 QTLs for these 6 traits under two distinct concentrations of salt, distributing on chromosomes 1, 2, 3, 4, 5, 6, 7 and 10. A total of 21 QTLs were found in 6 stable loci. A novel major QTL, qSL7 for shoot length on chromosome 7 was identified in two distinct concentrations. A chromosome segment substitution line (CSSL) harboring the qSL7 locus from PA64s with 93-11 background was developed and exhibited higher SL value, higher K + concentration, and lower Na + concentration compared to 93-11. With BC 5 F 2:3 derived from CSSL-qSL7/93-11, the qSL7 was fine mapped within a 252.9 kb region on chromosome 7 where 40 annotated genes located including, LOC_Os07g43530, which encodes a DNA-binding domain containing protein reported previously as a transcription factor playing a positive role in salt stress tolerance. Our study provides new genetic resources for improvement of salinity tolerance in rice breeding.

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Section: Discussionmentioning

confidence: 72%

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

Jahan

Zhang

et al. 2019

Plant Growth Regul

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“…Lack of tolerance to anaerobic germination (AG) results in insufficient energy supply for the growing embryo under oxygen deficit conditions caused by submergence [6]. Some rice genotypes have been reported to germinate under submerged conditions, however, only the tolerant genotypes survive by extending their coleoptiles or shoots above water, under declined oxygen levels [7].…”

Section: Introductionmentioning

confidence: 99%

Genetic Divergence Studies for Anaerobic Germination Traits in Rice (Oryza sativa L.)

Sudeepthi

Srinivas

Kumar³

et al. 2020

CJAST

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The present investigation was carried out to study the inherent genetic diversity of 107 rice genotypes towards development of rice varieties with tolerance for germination under anaerobic conditions for use in wet direct seeded rice cultivation system. The diversity was evaluated using multivariate analysis technique of Mahalanobis D2. The 107 rice genotypes studied were grouped into nine clusters. Twenty nine genotypes were grouped in cluster II followed by 27, 22, 10, 11 and 5 genotypes each in clusters I, III, IV, VI and cluster VII, respectively. The pattern of distribution of genotypes into various clusters was observed to be at random with no relation to geographical diversity. Results on inter-cluster distances revealed maximum diversity between genotypes of cluster VII and cluster IX, while intra-cluster distance was noticed to be maximum for cluster VI. Cluster IX had recorded higher cluster mean values for all the traits studied. Further, the traits, namely, shoot length, seedling dry weight and anaerobic response index together accounted for 62.45 per cent of the total genetic divergence in this study.

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“…Together, the TFGS QTLs explained 11.2% of PV. Three major QTLs on chromosomes 11 and 12 that (Han et al 2007), and qCD-9-3 and qCV-9 (Yang et al 2019) controlled the ESG-related trait VI-1 were qVI-1 11.2 , qVI-1 12.1 , and qVI-1 12.2 , with PV of 13.4%, 10.8%, and 10.2% and a LOD score of 5.21, 4.16, and 3.9, respectively (Table 5 and Fig. 3).…”

Section: Snp Markers For Qtl Mappingmentioning

confidence: 99%

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

et al. 2020

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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.

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Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

Cited by 55 publications

References 49 publications

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

Genetic Divergence Studies for Anaerobic Germination Traits in Rice (Oryza sativa L.)

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

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