Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

Li, Junzhou; Wang, Deping; Zhang, Hongliang; Hu, Guanglong; Li, Jinjie; Dai, Anyong; Liu, Lifeng

doi:10.1016/j.jgg.2011.08.005

Cited by 20 publications

(10 citation statements)

References 47 publications

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“…We then compared the QTLs identified by GWAS with QTLs detected previously by linkage mapping in two bi-parental crosses and found 10 [ 55 – 60 ] of the 21 RL QTLs and 23 [ 22 , 23 , 25 , 59 , 61 ] of the 96 RT QTLs were common ( S7 Table ) . We screened all 380 SNPs significantly associated with RL in 10 common QTL regions containing 102 candidate genes and found that 119 of these SNPs located in 35 genes in 7 QTLs showed differences between the parents of the bi-parental populations ( S8 Table ) .…”

Section: Resultsmentioning

confidence: 99%

“…The experiment was conducted twice as two replications from May 24 to June 15 and from June 23 to July 15 in 2014, during which the average daily temperatures fluctuated from 19.9°C to 31.7°C and from 23.9°C to 32.9°C, respectively. Seedlings were allowed to grow for 23 days and then five plants per variety were sampled and measured for RL, RT and root weight using a method described previously [ 23 ]. The mean values of all five plants of each accession were used as the input data in the data analyses.…”

Section: Methodsmentioning

confidence: 99%

“…1 , qRL7 and qRT9 [ 22 – 30 ]. OsbHLH120 that controls root thickness was cloned by map-based cloning using introgression lines [ 23 , 31 ]. Additionally, DRO1 affects deep rooting by controlling root angle and the mutation of SOR1 leads to observed deficiency in root gravitropic response and soil-surface rooting [ 30 , 32 ].…”

Section: Introductionmentioning

confidence: 99%

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Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

Zhao

Zhang

et al. 2018

PLoS Genet

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A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

Zhao

Zhang

et al. 2018

PLoS Genet

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“…(2016b) ; DRO3 : Uga et al. (2015) ; qSFR7 : Tomita and Fukuta (2019) ; qBRT7 a,b : Li et al. (2011) ; qRDR7 : Luo et al.…”

Section: A Low Tiller Gene Contributing To Plant Architectureunclassified

A Region on Chromosome 7 Related to Differentiation of Rice (Oryza sativa L.) Between Lowland and Upland Ecotypes

Uddin

Fukuta

2020

Front. Plant Sci.

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Due to global population expansion and climate change impacts, the development of a stable yielding variety that adapts well to unfavorable conditions for rice cultivation, can contribute to sustainable and stable production in rice (Oryza sativa L.). Understanding genetic differentiations to ecotypes for rice cultivations, such as upland, rainfed lowland, and irrigated lowland, is very important to develop the breeding materials for adapting to each environmental condition. The upland landrace variety basically has low tiller/panicle numbers and a large panicle, and the plant architecture is different from that of the lowland variety. The tiller and panicle numbers have been considered as one of the most difficult traits for genetic changes artificially in rice breeding. A low tiller recessive gene ltn2 originated from a New Plant Type variety, IR 65600-87-2-23, harboring segments from an upland variety, Ketan Lumbu (Tropical Japonica Group), was found on chromosome 7, and the other QTLs for culm length, culm weight, panicle length, panicle weight, seed fertility, harvest index, and soil surface rooting were also detected in the same chromosome region. These low tiller genes and the other QTLs were estimated to play an important role in developing the architecture for upland rice. Some QTLs for root growth angle, DRO3 and qSFR7, were also found in the same chromosome region from upland varieties categorized into the Tropical Japonica Group, and the QTLs may also be relevant to upland adaptation together with other traits. Previous studies using high throughput re-sequencing (whole genome variation data) of a large batch of rice accessions could identify the ecotype differentiated genomic regions (EDRs) and Ecotype differentiated genes (EDGs) such as Os07g0449700, a type response regulator, which is critical in upland adaptation in the same region of chromosome 7. Two selective loci, E3735 and E4208, for upland and lowland differentiation, and their corresponding genes Os07g0260000 and Os07g0546500 were also detected on chromosome 7 by drought-responding EST-SSRs. These findings indicate that the region on chromosome 7 is highly possible to related to the plant shoot and root architecture in the upland rice variety that has an important role and differentiates between upland and lowland ecotypes.

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“…When crops experience adverse conditions, the above three systems are mutually or independently initiated according to the level of stress. Under slight stress, maybe only retention water system was initiated in different accessions; under serious stress, these three systems may be initiated and interact with each other to respond to serious stress 23 – 26 . In our study, we chose the most serious period of drought stress to investigate the phenotype data consistent with our above analysis.…”

Section: Discussionmentioning

confidence: 99%

Parallel reaction monitoring revealed tolerance to drought proteins in weedy rice (Oryza sativa f. spontanea)

Han

Cui

et al. 2020

Sci Rep

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Drought is a complicated abiotic stress factor with severe effects on rice growth and production. Weedy rice is a valuable genetic resource that possesses a strong capacity for drought tolerance, cold tolerance, and salt tolerance, and is an excellent material for studying rice tolerance. Here, according to comprehensive tolerance to drought index D, accession WR16 was selected based on strong drought tolerance among 133 studied weedy red rice germplasms. WR16 was compared with Oryza sativa ssp. Japonica. cv. IAPAR-9, a reference genotype originating from Brazil. In addition, accession WR24 was classified as moderately tolerant to drought accessions. Transcriptomic and proteomic analyses were combined to identify 38 co-upregulated proteins related to drought tolerance, and targeted parallel reaction monitoring (pRM) was used to precisely quantify and verify nine proteins in the complex backgrounds. Result showed that six proteins were significantly (Fisher's exact P value < 0.05) related to drought tolerance in accessions WR16 and WR24. Among them, OS09T0478300-01, OS09T0530300-01, and OS01T0800500-01 formed a combined defense system to respond to drought stress in weedy rice. Results of these studies provide comprehensive information for precisely identifying and verifying tolerance to drought proteins and lay a solid theoretical foundation for research on drought tolerance mechanisms.

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Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

Cited by 20 publications

References 47 publications

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

A Region on Chromosome 7 Related to Differentiation of Rice (Oryza sativa L.) Between Lowland and Upland Ecotypes

Parallel reaction monitoring revealed tolerance to drought proteins in weedy rice (Oryza sativa f. spontanea)

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