Identification of Quantitative Trait Loci for Alkaline Tolerance at Early Seedling Stage under Alkaline Stress in <I>Japonica</I> Rice

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice.

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Detection of quantitative trait loci for phosphorus deficiency tolerance at soybean seedling stage

Euphytica ◽

10.1007/s10681-009-9880-0 ◽

2009 ◽

Vol 167 (3) ◽

pp. 313-322 ◽

Cited By ~ 53

Author(s):

Dan Zhang ◽

Hao Cheng ◽

Leiyue Geng ◽

Guizhen Kan ◽

Shiyou Cui ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Phosphorus Deficiency ◽

Seedling Stage ◽

Soybean Seedling ◽

Trait Loci

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Identification of quantitative trait loci for ABA responsiveness at the seedling stage associated with ABA-regulated gene expression in common wheat

Theoretical and Applied Genetics ◽

10.1007/s00122-010-1335-4 ◽

2010 ◽

Vol 121 (4) ◽

pp. 629-641 ◽

Cited By ~ 32

Author(s):

Fuminori Kobayashi ◽

Shigeo Takumi ◽

Hirokazu Handa

Keyword(s):

Gene Expression ◽

Quantitative Trait Loci ◽

Common Wheat ◽

Quantitative Trait ◽

Seedling Stage ◽

Trait Loci ◽

Regulated Gene Expression

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Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

Molecular Breeding ◽

10.1007/s11032-019-1090-4 ◽

2020 ◽

Vol 40 (1) ◽

Cited By ~ 5

Author(s):

S. Najeeb ◽

J. Ali ◽

A. Mahender ◽

Y.L. Pang ◽

J. Zilhas ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Low Temperature ◽

Quantitative Trait ◽

Root Length ◽

Stress Index ◽

Multiple Traits ◽

Main Effect ◽

Trait Loci ◽

Early Seedling ◽

Genomic Regions

AbstractAn attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I)1, qLTGS(I)1–2, qLTG(I)5, qLTGS(I)5, and qLTG(I)7) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT1, qLTT2, qLTT3, qLTT5, qLTT6, qLTT8, qLTT9, and qLTT11. A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.

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