QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses

Navabi, Alizera; Mather, D. E.; Bernier, Jérôme; Spaner, Dean; Atlin, G. N.

doi:10.1007/s00122-008-0904-2

Cited by 60 publications

(58 citation statements)

References 19 publications

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“…In the present study, out of the original F 2:3 population of 481 lines, only about 25% were genotyped. This selective genotyping approach can result in considerable cost savings in the detection of QTL with large effects on drought tolerance in rice (Navabi et al 2009). Different experimental approaches are needed when the objective is to detect only large-effect QTLs that may warrant fine-mapping, cloning, and deployment via marker-assisted backcrossing, rather than to catalog most of the regions affecting a trait in a particular cross (Bernardo 2008).…”

Section: Discussionmentioning

confidence: 99%

“…Selective genotyping can be a relatively low-cost approach to detecting QTL with large effects on important agronomic traits that can be integrated into ongoing breeding program operations (Navabi et al 2009). Venuprasad et al (2007Venuprasad et al ( , 2008 subjected breeding populations derived from crosses between droughttolerant upland rice varieties and susceptible lowland-adapted varieties to two generations of parallel selection for yield under drought-stressed and nonstressed conditions, demonstrating that direct selection for grain yield under severe drought stress was effective in increasing drought tolerance.…”

Section: Introductionmentioning

confidence: 99%

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Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population

et al. 2009

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Molecular marker loci responding to selection under drought stress were monitored in a rice breeding population obtained by crossing a tolerant parent (Apo) to a susceptible parent (IR64). The 40 highest-yielding lines under stress and nonstress conditions obtained after two cycles of divergent selection under drought stress and non-stress conditions, respectively were genotyped using 72 polymorphic and widely distributed SSR markers. Ten loci (RM572, RM6703, RM71, RM3387, RM5686, RM520, RM510, RM256, RM269 and RM511) showing highly significant allele frequency differences between the two sets were identified. Favorable alleles at eight of these loci came from the tolerant parent, and at two (RM3387 and RM510) from the susceptible parent (IR64). Effects of these loci on grain yield were tested in five independent experiments covering a range in soil moisture levels. Results showed that at six loci (RM572, RM6703, RM520, RM256, RM269, and RM511), Apo alleles had highly significant effects on grain yield in at least three of the four stress trials but only two of these loci (RM572 and RM511) also affected grain yield under non-stress conditions. In all these cases, the effects of loci generally increased with stress level. Apo alleles at these loci seem to enhance yield under stress mainly by increasing harvest index and reducing flowering delay. Large-effect quantitative trait loci (QTLs) affecting grain yield under upland drought stress have already been found previously in other populations near RM6703, RM520, and RM511. Thus, these regions appear to be important in explaining genetic variation for upland drought tolerance in rice.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population

et al. 2009

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“…In a population of 436 recombinant inbred rice lines segregating for a large-effect QTLs affecting grain yield under drought stress, Navabi et al (2009) reliably detected the QTLs by genotyping as few as 20 selected lines (4.5%). According to Ayoub and Mather (2002), genotyping of only 10% of the entire population was sufficient to detect all major QTLs.…”

Section: Genotypingmentioning

confidence: 99%

“…Selective genotyping is useful in situations in which full-population genotyping is too costly or not feasible, or where the objective is to rapidly screen large numbers of potential donors for useful alleles with large effects. Unidirectional selective genotyping (genotyping one side of the tail) is of particular interest for application within breeding programs, because it has the potential to permit QTL detection using superior progeny that have been retained under selection in breeding programs (Navabi et al 2009). This allows larger numbers of potential donors to be screened for useful alleles with effects across different backgrounds.…”

Section: Genotypingmentioning

confidence: 99%

The genetic dissection of quantitative traits in crops

Semagn¹,

Bjørnstad²,

Xu³

2010

Electron. J. Biotechnol.

111

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Most traits of interest in plant breeding show quantitative inheritance, which complicate the breeding process since phenotypic performances only partially reflects the genetic values of individuals. The genetic variation of a quantitative trait is assumed to be controlled by the collective effects of quantitative trait loci (QTLs), epistasis (interaction between QTLs), the environment, and interaction between QTL and environment. Exploiting molecular markers in breeding involve finding a subset of markers associated with one or more QTLs that regulate the expression of complex traits. Many QTL mapping studies conducted in the last two decades identified QTLs that generally explained a significant proportion of the phenotypic variance, and therefore, gave rise to an optimistic assessment of the prospects of markers assisted selection. Linkage analysis and association mapping are the two most commonly used methods for QTL mapping. This review provides an overview of the two QTL mapping methods, including mapping population type and size, phenotypic evaluation of the population, molecular profiling of either the entire or a subset of the population, marker-trait association analysis using different statistical methods and software as well as the future prospects of using markers in crop improvement.

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“…IRRI research has shown that variation for the trait can be strongly influenced by alleles of a relatively small set of QTLs with large effects. We have developed efficient "selective genotyping" strategies that allow many potential donors to be searched quickly and inexpensively for these valuable genes (Navabi et al, 2009). This allows the search for useful alleles to be quickly narrowed down to small chromosome segments suitable for bioinformatics analysis.…”

Section: A Strategy For Improving Drought Resistancementioning

confidence: 99%

Drought Resistance Improvement in Rice: An Integrated Genetic and Resource Management Strategy

Serraj

McNally

Slamet‐Loedin

et al. 2011

Plant Production Science

209

119

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Drought is the major constraint to rice production in rainfed areas across Asia and subSaharan Africa. In the context of current and predicted water scarcity, increasing irrigation is generally not a viable option for alleviating drought problems in rainfed rice-growing systems. It is therefore critical that genetic management strategies for drought focus on maximum extraction of available soil moisture and its effi cient use in crop establishment and growth to maximize biomass and yield. Extensive genetic variation for drought resistance exists in rice germplasm. However, the current challenge is to decipher the complexities of drought resistance in rice and exploit all available genetic resources to produce rice varieties combining drought adaptation with high yield potential, quality, and resistance to biotic stresses. The strategy described here aims at developing a pipeline for elite breeding lines and hybrids that can be integrated with efficient management practices and delivered to rice farmers. This involves the development of high-throughput, highprecision phenotyping systems to allow genes for yield components under stress to be effi ciently mapped and their effects assessed on a range of drought-related traits, and then moving the most promising genes into widely grown rice mega-varieties, while scaling up gene detection and delivery for use in marker-aided breeding.

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QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses

Cited by 60 publications

References 19 publications

Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population

Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population

The genetic dissection of quantitative traits in crops

Drought Resistance Improvement in Rice: An Integrated Genetic and Resource Management Strategy

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