QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping

Baltazar, Miriam D.; Ignacio, John Carlos I.; Thomson, Michael J.; Ismail, Abdelbagi M.; Mendioro, Merlyn S.; Septiningsih, Endang M.

doi:10.1007/s10681-014-1064-x

Cited by 69 publications

(54 citation statements)

References 42 publications

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“…The largest QTL, qAG7.1, located on chromosome 7 explained 31.7% of the variation, having an LOD score of 14.5 (Septiningsih et al 2013). Similarly, a major QTL for AG derived from Nanhi, an aus landrace from India, named qAG7, was detected on chromosome 7 with an LOD of 13.93 and 22.3% of the phenotypic variance explained (Baltazar et al 2014). In subsequent research, the KHO-derived qAG9-2 was fine mapped to a * 50 kb region on chromosome 9 that contains four genes and, of these, the trehalose-6-phosphate phosphatase gene, OsTPP7, was identified as the genetic mechanism underlying qAG9-2 (Kretzschmar et al 2015).…”

Section: Discussionmentioning

confidence: 97%

“…The population distribution was skewed towards susceptibility, possibly as a consequence of the consistently hypoxic screening conditions in which the DO value was maintained at \ 4.0 ppm until the coleoptiles emerged from water surface. Screening methods, which involve flooding with 10 cm of water depth, are commonly used to evaluate the AGtolerance level of rice seedlings (Angaji et al 2010;Septiningsih et al 2013;Baltazar et al 2014), however, none report monitoring oxygen levels in the floodwater. Flooding in combination with the maintenance of consistent hypoxic conditions is a new evaluation method for AG tolerance used in this study.…”

Section: Discussionmentioning

confidence: 99%

“…In particular, the largest QTL was on chromosome 7, having a LOD score of 14.5 and an R 2 of 31.7%; this was further confirmed using a BC 2 F 3 population. Baltazar et al (2014) detected four QTLs related to AG tolerance using a 384-plex SNP Indica/Indica set on the Illumina BeadXpress reader. A major QTL, qAG7, for AG derived from the cultivar Nanhi, an upland landrace from India, was detected on chromosome 7 with an LOD of 13.93 and explaining 22.3% of the phenotypic variance.…”

Section: Introductionmentioning

confidence: 99%

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Identification of QTLs for tolerance to hypoxia during germination in rice

Kim

Reinke

2018

Euphytica

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Direct seeding of rice as a method of crop establishment is increasingly being adopted by farmers as a means of saving labor and reducing costs. However, the method often results in a poor environment for germination as excessive water levels after seeding can cause poor seedling establishment and a concomitant reduction in yield potential, especially in submergence-prone areas. In this study, we discovered QTLs associated with tolerance of anaerobic germination (AG) in new genetic accessions using genotypic data derived from the Illumina 6K SNP chip. The mapping population developed for QTL analysis comprised 285 F 2:3 plants derived from a cross between Tai Nguyen and Anda. In order to evaluate AG tolerance within the mapping population, phenotyping was carried out under anaerobic conditions for 21 days. Three QTLs associated with AG tolerance were identified in the population, qAG1a and qAG1b on chromosome 1 and qAG8 on chromosome 8 using composite interval mapping (CIM). The percentage of variance explained by these QTLs ranged from 5.49 to 14.14%. The lines with three QTLs (qAG1b ? qAG1a ? qAG8) demonstrated an approximate 50% survival rate under anaerobic conditions, while lines with two QTLs including qAG1b demonstrated survival rates of 36 and 32% after the treatment, respectively. The QTLs detected in this study may be used to improve AG tolerance during germination and may be combined with other QTLs for anaerobic germination to enhance adaptation to direct seeding and to broaden the understanding of the genetic control of tolerance of germination under anaerobic conditions.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of QTLs for tolerance to hypoxia during germination in rice

Kim

Reinke

2018

Euphytica

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“…In other cases, determinants may not be equally effective throughout development. For example, anaerobic rice germination for robust early establishment is an important agronomic trait that does not seem to overlap with the submergence tolerance of older seedlings 142 .…”

Section: Winter Varietiesmentioning

confidence: 99%

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

2015

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Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.

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“…Likewise, quantitative traits loci and genes for tolerance to various abiotic stresses, including drought, salinity, submergence during vegetative stage, submergence during germination, stagnant flooding and iron toxicity have been identified and used in molecular breeding programs Thomson et al 2010;Iftekharuddaula et al 2011;Septiningsih et al 2012;Septiningsih et al 2013b;Baltazar et al 2014;Dixit et al 2014;Kretzschmar et al 2015;Toledo et al 2015;Gonzaga et al 2016;Iftekharuddaula et al 2016a;Singh et al 2016). In addition, elite breeding lines tolerant to multiple abiotic stresses have been developed through conventional breeding (Gregorio et al 2002;Kumar et al 2008;Collard et al 2013a;Collard et al 2013b).…”

Section: Introductionmentioning

confidence: 99%

Development of High-Yielding Rice Varieties Suitable for Swampy Lands in Indonesia

Rumanti¹,

Nugraha²,

Wening³

et al. 2016

Plant Breed. Biotech.

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Productivity of swampy land rice varieties in Indonesia remains low due to abiotic and biotic stresses. Iron toxicity, submergence and long-term flooding are common problems that affect plant growth, sometimes leading to total crop loss. Meanwhile, rice blast, rice tungro virus (RTV), and bacterial leaf blight (BLB) can also lead to severe yield loss. These stresses could be overcome by an integrative approach of cultural practices and planting multi-stress tolerant rice. Here we describe the development of new high-yielding varieties that are adapted to the swampy land environments in Indonesia with multi-stress tolerance to diverse abiotic and biotic stresses. Multi-environmental trials were performed in nine locations to screen for several abiotic and biotic stresses in the field and greenhouse in 2012 and 2013. This study identified promising rice lines that had high grain yield as well as tolerance to iron toxicity and submergence, resistance to BLB and RTV, and good grain quality. The best line was B11377F-MR-34-2, derived from a double cross among Cinglonik, IRBB7, Mamberamo and IR64. It was confirmed that this advanced breeding line carries the submergence tolerance gene, SUB1, through expression analysis of the SUB1A gene. Another promising line was B11586F-MR-11-2-2, having iron toxicity tolerance, resistance to RTV, and high milling recovery. Moreover, these lines have passed the Indonesian national variety release committee and have been named as Inpara8 and Inpara9, and are targeted for dissemination and adoption in the swampy areas.

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QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping

Cited by 69 publications

References 42 publications

Identification of QTLs for tolerance to hypoxia during germination in rice

Identification of QTLs for tolerance to hypoxia during germination in rice

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

Development of High-Yielding Rice Varieties Suitable for Swampy Lands in Indonesia

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