Analytical and numerical comparisons of two methods of estimation of additive × additive interaction of QTL effects

Bocianowski, Jan

doi:10.1590/s0103-90162012000400002

Cited by 19 publications

(14 citation statements)

References 34 publications

(30 reference statements)

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“…After the analysis of the HT DH lines in the four cases (NM in MB92, H in ON93a, L in ON92a and L in ON92b), epistatic effects showed only loci with significant additive effects-differences aa-aa g equal to 0 (compared with results presented by Bocianowski 2012b). In 38 cases, the epistatic effects calculated as locus 9 locus interactions were non-significant (see Bocianowski 2012b). In this paper, those effects were statistically significant different aa-aa g = aa (Table 2).…”

Section: Discussionmentioning

confidence: 56%

“…Therefore, CDO105-BCD135 might be a pleiotropic pair of loci or very tight linkage. Additionally, in the Tables 1, 2 and 3 are presented differences between epistatic effects assessed using all loci (aa) and epistatic effects assessed using only loci with significant additive effects (aa g ), it should be noted that the aa g values have been presented in previous studies (Bocianowski 2008(Bocianowski , 2012b.…”

Section: Resultsmentioning

confidence: 99%

“…So, by way of illustration, a 6-7.8 6.6-8.4 6.5-11.9 6.9-8.7 6.5-8.5 -6.5-9.2 Euphytica (2014) 196:105-115 111 Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. ID91 Aberdeen, Idaho, 1991;ID92 Tetonia, Idaho, 1992;MA92 Brandon, Manitoba, 1992;MN92 Crookston, Minnesota, 1992;MTd91 Bozeman, Montana, dry, 1991;MTd92 Bonzeman, Montana, dry, 1992;MTi91 Bozeman, Montana, irrigated, 1991;MTi92 Bozeman, Montana, irrigated, 1992;NY92 Ithaca, New York, 1992;ON92 Guelph, Ontario, 1992;OR91 Klamath Falls, Oregon, 1991;Kg92 Goodlae, Saskatchewan, 1992;SKg93 Kcfr, Saskatchewan, 1992;SKo92 Outlook, Saskatchewan, 1992;WA91 Pullman, Washington, 1991;WA92 Pullman, Washington, 1992; AA alpha amylase; DP diastatic power; GP grain protein; GY grain yield; H height; HD heading date; L lodging; ME malt extract a aa g values from previous studies (Bocianowski 2012b) Euphytica (2014 …”

Section: Discussionmentioning

confidence: 99%

“…Estimation of additive 9 additive epistatic interactions (aa) was based on the assumption that the genes responsible for the trait were closely linked to observed molecular marker (Bocianowski 2012b). A two-stage algorithm was employed for the selection of significant pairs of loci (markers) with significant epistasis interaction effects.…”

Section: Genetic Modelmentioning

confidence: 99%

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Estimation of epistasis in doubled haploid barley populations considering interactions between all possible marker pairs

Bocianowski

2013

Euphytica

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Epistasis, is the interaction between alleles from two or more loci determining complex traits, and thus plays an important role in the development of quantitative traits of crops. In mapping studies of inbreeding species epistasis is usually defined as the interactions between quantitative trait loci with significant additive gene effects. Indeed, in many studies, genes with small effects do not come into the final model and thus the total epistasis interaction effect is biased. Many loci may not have a significant direct effect on the trait under consideration, but they may still affect trait expression by interacting with other loci. In this paper the benefits of using all loci, not only the loci with significant main effects, for estimation of the epistatic effects are presented. The particular examples are with doubled haploids lines and so are restricted to homozygotes and thus additive genetic effects and additive 9 additive interactions. Numerical analyses were carried out on three populations of doubled haploid lines of barley (Hordeum vulgare L.): 120 doubled haploid lines from the Clipper 9 Sahara 3771 cross, 145 doubled haploid lines from the Harrington 9 TR306 cross and 150 doubled haploid lines from the Steptoe 9 Morex cross. In total, 157 sets of observations were analyzed and altogether 728 pairs of loci were observed for the three datasets.

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Section: Discussionmentioning

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Genetic Modelmentioning

confidence: 99%

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Estimation of epistasis in doubled haploid barley populations considering interactions between all possible marker pairs

Bocianowski

2013

Euphytica

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“…The effect of additive-by-additive interaction (epistasis) was estimated on the basis of phenotypic observations according to Bocianowski (2012a). This method requires the identification of groups of extreme lines, i.e., lines with the minimal and maximal expression levels of the trait under consideration.…”

Section: Qtl Detectionmentioning

confidence: 99%

<b>Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

et al. 2017

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ABSTRACT. Barley (Hordeum vulgare L.) is considered a good genetic model for evaluating mechanisms of drought tolerance, and it is the most important threat to crop production worldwide. This study aimed to identify single-nucleotide polymorphisms (SNPs) associated with agronomic, morphological and physiological traits in a population of 137 recombinant chromosome substitution lines (RCSL) of barley, which were evaluated under rainfed conditions, in Cauquenes, southern Chile (35°58' S, 72°17' W). The annual precipitation was 299 mm during the growing season. Fifty-two significant QTLs were detected for the studied traits, which explained between 5% and 13.8% of the phenotypic variation. A genomic region on chromosome 1H (that comprises SNPs 2711-234 and 1923-265) accounted for 13.4% and 13.8%, respectively, of the grain yield variation. In addition, SNPs 8388-578 and 7639-122 on the chromosome 5H had a moderate effect, explaining 12.8% of the plant height variation. Moreover, some SNPs were associated with more than one trait, and clusters of QTLs for yield and related traits were also found. Finally, the QTLs identified in the present study are of particular interest for barley-breeding purposes under rainfed conditions. Keywords:Hordeum vulgare, mixed model, recombinant chromosome substitution lines, segregation distortion.Identificação de QTL associados a características agronômicas, morfológicas e fisiológicas em cevada sob condições de sequeiro, usando marcadores SNP RESUMO. Cevada (Hordeum vulgare L.) é uma cultura modelo para a avaliação genética dos mecanismos de tolerância à seca; a ameaça mais importante para a produção agrícola a nível mundial. Objetivou-se identificar polimorfismos de nucleotídeo único (SNP) associados a características agronômicas, morfológicas e fisiológicas numa população de 137 linhas recombinantes com substituição cromossômica (RCSL) de cevada, avaliadas sob condições de sequeiro, em Cauquenes, sul do Chile (35°58' S, 72°17' O). A precipitação anual foi de 299 mm durante o período vegetativo. Cinquenta e dois QTLs foram encontrados para as características estudadas, explicando entre 5% e 13.8% da variação fenotípica. A região genômica no cromossomo 1H (que compreende os SNPs 2711-234 e 1923-265) foi responsável de ~13% da variação no rendimento de grãos. Além disso, os SNPs 8388-578 e 7639-122 no cromossomo 5H teve um efeito moderado, explicando 12,8% da variação para altura da planta. Além disso, alguns SNPs foram associados com mais de uma característica, e grupos de QTLs para rendimento de grãos e características relacionadas também foram encontrados. Finalmente, os QTLs identificados no presente estudo podem ser de particular interesse para fins de melhoramento de cevada em ambiente de sequeiro.Palavras-chave: Hordeum vulgare, modelo misto, linhas recombinantes com substituição cromossômica, distorção de segregação.

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Quantitative trait loci from identification to exploitation for crop improvement

Kumar

Gupta

et al. 2017

Plant Cell Rep

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Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.

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Analytical and numerical comparisons of two methods of estimation of additive × additive interaction of QTL effects

Cited by 19 publications

References 34 publications

Estimation of epistasis in doubled haploid barley populations considering interactions between all possible marker pairs

Estimation of epistasis in doubled haploid barley populations considering interactions between all possible marker pairs

<b>Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

Quantitative trait loci from identification to exploitation for crop improvement

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