Use of LOD score technology in mapping quantitative trait loci in plants

Kocherina, N. V.; Артемьева, А. М.; Chesnokov, Yu. V.

doi:10.3103/s1068367411030098

Cited by 8 publications

(4 citation statements)

References 7 publications

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“…), which are explained by the QTL data, for each trait and population, was performed using the MAPQTL 6.0 [37]. The significance of each LOD was established by a permutation test (1000 repetitions) [38]. The correlation coefficient "trait-marker" was calculated for the 95% significance level as a statistically significant linkage of the marker locus with the QTL, which determines the studied trait, based on the empirically obtained variances for each pair of trait-marker [39].…”

Section: Statistical Processing Of the Obtained Results And Qtl Analysismentioning

confidence: 99%

“…In this case, the critical value 3 will correspond to the maximum value of the type I error (at p < 0.001), and if a very high particular (individual) type I error is selected, for example 5%, then a high level of cohesion will be reliably found randomly. At the same time, both major and minor QTLs are often localized in the same positions in different experiments and even in different years of experiments; therefore, an LOD score below 3 can also be taken into account [38]. It is also likely that the low LOD score for some of the identified QTLs is due to statistical reasons (limited sample size), since only lines adapted to light culture conditions were included in the estimate.…”

Section: Quantitative Trait Loci Mapping (Qtl Analysis)mentioning

confidence: 99%

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QTL Analysis of the Content of Some Bioactive Compounds in Brassica rapa L. Grown under Light Culture Conditions

et al. 2021

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The article presents the results of biochemical and QTL (Quantitative Trait Loci) analysis of dry matter content, nutrient and biologically active compounds: sugars, ascorbic acid, chlorophylls a and b, anthocyanins and carotenoids in populations of doubled haploid lines of leaf, root crops, and oilseeds of the Brassica rapa L. species grown in optimal light culture conditions, but with different photoperiod durations. The purpose of this study was to evaluate the effect of the photoperiod on the transition to bolting and the accumulation of biologically active substances, as well as how the localization and identification of chromosomal loci determined the content of certain phytochemicals. The influence of the length of daylight hours on the content of components of the biochemical composition was assessed. It was shown that growing under conditions of a 16 h photoperiod increased the content of dry matter, sugars, vitamin C, and anthocyanins. On the contrary, the content of photosynthetic pigments was higher under the conditions of a 12 h photoperiod. Valuable lines that can be sources of biologically active compounds were revealed. Based on the results of the obtained data, 102 QTLs were mapped, which determine the manifestation of the studied biochemical quality traits in the B. rapa doubled haploid lines under conditions of short and long daylight hours. Molecular markers genetically linked to the selected QTLs were determined. It was revealed that the identified loci controlling all the studied biochemical traits were mainly in the fifth, sixth, seventh, and ninth linkage groups, which correlated with the data obtained in the field and greenhouse. Most of the identified loci controlled several studied traits simultaneously. The identified QTLs and identified molecular markers are of interest for further study of the genetic control of the economically valuable traits determined by them and for the implementation of marker-assisted selection in B. rapa. The data obtained can be used in genetic and breeding work, including for the obtaining of new genotypes, lines and cultivars with a valuable biochemical composition, adapted for cultivation under specific photoperiodic conditions.

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Section: Statistical Processing Of the Obtained Results And Qtl Analysismentioning

confidence: 99%

Section: Quantitative Trait Loci Mapping (Qtl Analysis)mentioning

confidence: 99%

QTL Analysis of the Content of Some Bioactive Compounds in Brassica rapa L. Grown under Light Culture Conditions

et al. 2021

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“…For this purpose, the CIM Zmapqtl module model 6 with a window size of 10 cM and the 5 markers for the background control were used (Wang et al 2012). QTLs were identified using LOD score of C 3 as the threshold (probability of 1000-1) (Kocherina et al 2011). The proportion of observed phenotypic variation explained (PVE) due to a particular QTL was estimated by the coefficient of determination (R 2 ) using maximum likelihood approach (Basten et al 1994).…”

Section: Composite Interval Mappingmentioning

confidence: 99%

Identification of modifiers of the plant height in wheat using an induced dwarf mutant controlled by RhtB4c allele

Agarwal

Balyan

Gupta

2020

Physiol Mol Biol Plants

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In wheat, 25 Rht genes for dwarfness are known, which include both, GA-insensitive and GA-responsive genes. The GA-insensitive Rht genes have been widely used, although, their suitability under abiotic stress conditions has been questioned. This necessitated a search for alternative GA-responsive, spontaneous and induced dwarfing genes. We earlier reported an induced dwarf mutant ('dwarf mutant-3 0 ; 44 cm), and the mutant allele was named Rht4c allele (2BL). This dwarf mutant was not suitable for cultivation due to its extra dwarf nature. Therefore, we searched for naturally occurring QTLs, which would modify the phenotype of 'dwarf-mutant-3 0 using 'mutant-assisted gene identification and characterization' (MAGIC) approach. For this purpose, the 'dwarf mutant-3 0 was crossed with a tall wheat cv. NP114 and homozygous mutant F 2 plants (* 25% of the progeny) were selected, which were phenotyped for plant height and genotyped using SSR markers. The data were utilized for QTL analysis and plant height. Six modifier QTLs were identified on chromosomes 2A, 2B and 4A. Two QTLs each on 2A and 2B were responsible for increase in plant height (described as 'enhancer modifiers'), whereas the remaining two QTLs located on 4A were responsible for reducing the plant height (described as 'suppressor modifiers'). It was hypothesized that the enhancer QTLs could be exploited for the development of semi-dwarf high yielding genotypes containing Rht4c allele. This is the first study of its kind in wheat demontsrating that the MAGIC approach could be used for identification of modifiers of the mutant phenotypes of other traits for wheat improvement.

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“…), которые объясняются соответствующим QTL, для каждой изоформы эстеразы в каждой популяции. Значимость LOD устанавливали в тесте пермутации (1000 повторений) (36).…”

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QTL MAPPING OF ESTERASE ISOZYME FORMS IN Brassica rapa L. MATURE SEEDS

Rudakova¹

2019

s-h. biol.

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С 1960-х годов изоферменты хорошо известны как одни из наиболее распространенных биохимических маркеров. Установление общей изменчивости изоферментных систем и выявление их генетического контроля сохраняют актуальность, позволяя вскрывать тонкие механизмы взаимоотношения организма с окружающей средой и гомеостаза и разрабатывать эффективные биохимические маркеры для экспресс-оценки генетически и селекционно значимого материала. В представленной работе нами впервые идентифицированы и картированы локусы хромосом, отвечающие за проявление активности 13 различных изоформ эстераз зрелых семян у Brassica rapa L. В исследовании использовали линии удвоенных гаплоидов двух картирующих популяций -DH30 и DH38. Все выявленные изоформы эстераз по электрофоретической подвижности подразделялись на три группы. Группа изоформ А1-А3 обладала большой молекулярной массой и малой электрофоретической подвижностью, группа изоформ В1-В7 характеризовалась средней молекулярной массой и проявляла среднюю электрофоретическую подвижность, группу С1-С3 составляли изоформы с малой молекулярной массой и, соответственно, наибольшей электрофоретической подвижностью. Каждая из родительских форм (как и каждая из исследованный линий картирующих популяций) имела уникальный электрофоретический спектр изоформ эстераз. На основании полученных электрофоретических данных для обеих популяций был проведен QTL-анализ и установлены локусы хромосом, определяющие проявление каждой изоформы эстеразы, выявленной у линий картирующих популяций DH30 и DH38. Использованный подход множественного интервального QTLкартирования (composite interval mapping) в сочетании с тестом пермутации (1000 повторений) при уровне статистической значимости p < 0,05 позволил идентифицировать и локализовать на хромосомах локусы (QTL, quantitative trait loci), определяющие проявление всех изоформ эстераз, идентифицированных методом гель-электрофореза. Исключение составили изоформы А1 для популяции DH38 и изоформы В7 для популяции DH30, для которых мы не получили результатов QTLанализа из-за малого объема исходных данных по этим изоформам у соответствующей картирующей популяции. Всего картировали 35 QTL изоформ эстераз в случае картирующей популяции DH30 и 39 QTL для популяции DH38. В результате проведенного QTL-анализа выявили молекулярные маркеры, генетически сцепленные с идентифицированными локусами, и рассчитали процент фенотипической изменчивости, определяемый каждым из выявленных QTL. По данным изоферментного анализа был проведен расчет гетерозиготности для обеих популяций в каждом локусе H l и общей гетерозиготности H общ. , а также дисперсии гетерозиготности Var(H l ) по одному локусу и дисперсии средней гетерозиготности внутри каждой из популяций Var(H общ. ). Выявленная гетерозиготность рассматривалась как средняя порция локусов с двумя различными аллелями в одном локусе у одной особи и могла быть определена как наблюдаемая гетерозиготность, характеризующая часть генов, по которым изучаемая популяция гетерозиготна. Показано, что в изученных популяциях линий удвоенных гаплоидов QT...

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Use of LOD score technology in mapping quantitative trait loci in plants

Cited by 8 publications

References 7 publications

QTL Analysis of the Content of Some Bioactive Compounds in Brassica rapa L. Grown under Light Culture Conditions

QTL Analysis of the Content of Some Bioactive Compounds in Brassica rapa L. Grown under Light Culture Conditions

Identification of modifiers of the plant height in wheat using an induced dwarf mutant controlled by RhtB4c allele

QTL MAPPING OF ESTERASE ISOZYME FORMS IN Brassica rapa L. MATURE SEEDS

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