Heterosis: current advances in the search for molecular mechanisms

Heterosis as the increased performance of hybrid progeny compared to their inbred parents is one of the most intriguing phenomena in genetics. The first attempts to find out about underlying mechanisms were based on theoretical models, which were useful, but could not characterize this unique phenomenon as a whole. With the advent of molecular markers great efforts were made to identify genomic regions causing heterotic response and clarify prospects of using information about molecular divergence of parental forms as a criterion for the prediction of F1 performance. Despite some achievements, the effec-tiveness of both molecular divergence and prospective heterotic QTL for practical goals was limited, confirming that genetic heterogeneity is necessary, but not sufficient to produce perfect phenotype. Current methodological tools of functional genomics and related disciplines have provided new opportunities for searching for mechanisms of heterosis at different levels in the context of relative importance of dominance, overdominance and epistasis. To date, differences in genome organization, gene expression and epigenetic status have been found between hybrids and their parents. At the genomic level, some QTLs associated with heterosis were identified and the impact of DNA divergence on F1 performance was evaluated. At the level of transcriptome, it was shown that heterosis in hybrids occurs along with changes in gene expression regulation under the influence of circadian clock genes. Several studies have been conducted to clarify the role of epigenetic DNA modification and genomic imprinting in the manifestation of heterosis. Taken together, data indicates that heterosis cannot been explained by a single common mechanism, because this complex phenomenon involves many components, a cumulative effect of which leads to the formation of an outstanding phenotype

Theoretical aspects of heterosis

The phenomenon of heterosis, known as superior performance of hybrid organism compared with either of their parents, has been exploited by agricultural practices in the production of various crops since the beginning of the last century; however, its genetic basis has remained obscure. With experimental data obtained from the study of maize hybrids, and mathematical calculations, some genetic models have been proposed to explain heterosis from various types of gene interaction, such as dominance, over-dominance and epistasis. However, any of the proposed concepts has weak points, which place limitations on the possibility of overall interpretation of heterotic response in F1. In this review we gather a brief account of findings from various studies for critical evaluation of the main theoretical concepts based on the information accumulated to date by genetics and molecular biology and focused on particular mechanisms acting for specific traits. We discussed some aspects concerning the role of mutation loads in the formation of heterotic phenotype. Also, we gathered a brief account of findings for interpretation of genetic effects due to linkage and non-allelic genes’ interactions that make nuances to analysis of dominance and over-dominance. We have provided information about combining ability, its practical application in the context of the concept of heterotic groups. Here we also discussed some aspects of “genotype–environment” interaction. Recent advancements in genetics and molecular biology indicate the importance of various types of gene action for heterosis and confirm the necessity of systemlevel approaches to understanding this unique phenomenon

Informative EST-SSR markers for genotyping and intraspecific differentiation of Brassica oleracea var. capitata L.

Brassica oleraceae var. capitata L. is characterized by a high level of intraspecific heterogeneity due to some biological features that cause difficulties for breeding creating genetically homogenous forms and maintaining their genetic purity. Microsatellites (SSR) are highly polymorphic markers of plant genomes and represent one of the most effective tools for assessing genetic polymorphism. Among microsatellites, EST-SSR are most interesting, because they are directly linked to the expressed sequences and for that reason are widely used for analysis of genetic diversity and population structure. In this work, we studied the effectiveness of the use of transferable EST-SSR markers for both analyzing white cabbage diversity and genotyping pure lines. As a result, 15 microsatellite loci were characterized for the information content, allelic frequencies and heterogeneity levels. The effective multiallelic markers (Bo20TR, BoDCTD4, BoPC34, BoPLD1, BoCalc, BoPC15) with high information content (PIC > 0.7) that could be successfully used for analysis of inter- and intravarietal polymorphism in B. oleracea var. capitata were identified. It has been shown that intervarietal polymorphism expressed as the allelic diversity of EST SSR loci greatly facilitates varietal identification and typing of individual plants for breeding purposes. Based on the SSR-evaluation and subsequent clustering, the genetic structure of the breeding collection was identified, which showed that most experimental forms, in spite of different origin, have a common ancestral genetic basis. The identified donors of rare alleles could potentially be a source of valuable genetic segregation for further B. oleracea breeding improvement

SNP-АНАЛИЗ ГЕНЕТИЧЕСКОГО РАЗНООБРАЗИЯ ПШЕНИЦЫ БЕЛАРУСИ

We used a high-throughput array to evaluate the diversity of hexaploid wheat growing in Belarus under the breeding program through 384 gene-associated SNPs. The gene pool of winter and spring varieties are significantly different in frequency of 248 variants from 174 SNPs. The genetic structure of the Belarusian population of wheat has appeared similar to the Russian and Ukrainian varieties and is essentially different from west-European varieties. But it has a high variability and, consequently, a good genetic potential for the improvement through breeding.Проведено изучение генетического разнообразия пшеницы Беларуси на основе высокопропускного SNP маркирования. В целом из 384 использованных маркеров в исследуемой коллекции типирован 331 локус. Генофонды озимых и яровых сортов достоверно различаются по частотам 248 вариантов 174 SNP. Генетическая структура белорусских сортов обнаруживает значительное сходство с образцами российской и украинской селекции, но при этом обладает значительным запасом разнообразия, которое представляет хороший потенциал для создания новых высокопродуктивных адаптированных форм

Allelic and epigenetic DNA variation in relation to F1 heterosis manifestation in F1 hybrids of Capsicum annuum L.

Managing F1 heterosis is one of the major objectives in hybrid crop breeding programs. The classical theory considers the heterozygosity in F1 hybrids to be the main factor contributing to heterosis and therefore presumes a linear relationship between the value of genetic polymorphisms in parental lines and the heterotic response of their F1 offspring. Therefore, the genetic diversity information is viewed as a tool for selection of promising cross-combinations, but results published by different researchers are inconsistent. In this work, we studied the contributions of structural and nonstructural DNA polymorphisms to F1 heterosis manifestation. We used SSR and methyl-sensitive AFLP (MSAP with HpaII and MspI izoshisomers) protocols for obtaining specific patterns for heterotic and nonheterotic F1 hybrids of sweet pepper (Capsicum annuum L.) from a Belarusian breeding program. We found out that a certain portion of heterosis for yield-related traits might be explained by the polymorphism revealed by SSR analysis. According to our data, the total number of polymorphic SSR loci and the ratio of polymorphic and nonpolymorphic loci demonstrate a significant predictive value and can serve as additional prognostic criteria for the selection of promising cross-combinations. From the MSAP assay, we found a relationship between heterosis and the numbers of methylated and nonmethylated DNA loci for yield traits. Our results indicate that cross-hybridization may favor epiallelic modifications in F1 hybrids, presumably responsible for heterosis. Thus, epigenetic DNA variation may explain the absence of a linear relationship between the level of structural DNA divergence and F1 heterosis, as well as the manifestation of heterosis in crosses of related (genetically similar) accessions

ВКЛАД МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКОЙ ДИВЕРГЕНЦИИ КАПУСТЫ БЕЛОКОЧАННОЙ В РЕАЛИЗАЦИЮ ПРОДУКТИВНОГО ПОТЕНЦИАЛА ГИБРИДОВ F1

The prediction efficiency of white cabbage F1 hybrid performance based on ISSR and RAPD markers was carried out. In result molecular-genetics evaluation of white cabbage collection, five divergent lines were selected and tested by full diallel (5×5) mating design. Through analysis relationship genetic divergence of parental lines and F1 hybrid performance the significant correlations (r > 0.5) were found for the main yield components. Yield potential of half-diallel F1 hybrids was predetermined total GD by 67.2 % (R = r2), whereas no significant associations were found for reciprocal F1. Consequently, heterotic response does not simply result from the overall genetic diversity within a hybrid, but is likely only diversity at some specific loci causing the formation of superior F1 genotype with high expression of the traits.Проведено изучение эффективности предсказания продуктивного потенциала гибридов F1 капусты белокочанной на основе оценки генетической дивергенции исходных форм, величину которой рассчитывали с использованием ISSR- и RAPD-маркеров. В результате молекулярно-генетического исследования селекционной коллекции отобрали 5 линий, которые прошли испытание в системе полного диаллельного скрещивания. Гибриды F1 в большинстве комбинаций достоверно превосходили родителей по основным хозяйственно ценным признакам. Анализ сопряженности дивергенции родительских форм с компонентами урожая F1 показал, что существуют достоверные корреляции (r > 0,5) между уровнем GD и основными компонентами продуктивности. При этом продуктивный потенциал прямых гибридов F1 на 67,2 % (R = r2) предопределен общей GD родительских форм, тогда как для реципрокных F1 статистически значимых связей не обнаружено. Вероятно, формирование высокопродуктивного гетерозисного генотипа не настолько связано с общей гетерогенностью гибридного генома, как с полиморфизмом в отдельных специфических локусах, которые обусловливают высокую экспрессию признаков в F1

Генетический анализ останков из погребений XVII–XVIII вв. костела Божьего Тела в Несвиже

During archaeological excavation in the territory of the Corpus Christi Church in Nesvizh, the regular burials dated to the 17th–18th centuries were discovered. The genetic material extracted from the bones of seven unidentified individuals was analyzed using the forensic genetics approaches, including STR profiling and DNA phenotyping. The genetic examination revealed that the remains of three samples (#1, #2, #6) belonged to women, and the four others (#3, #4, #5, and #7) belonged to men. Autosomal STR-data and Y-chromosomal profiles were obtained for five samples. The kinship analysis excluded that woman #1 and men #3, #4, #5, #7 were first-degree relatives. According to the Y-STR profiles, men #3, #4, #7 referred to the haplogroup R1a, the haplotype of individual #5 corresponded to I2. The both haplogroups are widely represented in Eastern Europe, which, with a high degree of probability, suggests the Slavic origin of the individuals under investigation. To predict eye and hair color, we used the HIrisPlex DNA phenotyping system. The analysis gave the satisfactory results for woman #1 and man #7. In correspondence to the allelic variants of the 24 SNP system, woman #1 had an intermediate type of iris pigmentation and dark blond hair (p = 0.635) with dark shade (0.639), light skin tone, low tendency to sunburn, and a high probability of freckles and pigmented spots of the skin. For male #7, the HIrisPlex model predicted blue eye color with a high probability (p = 0.915), as well as blond hair color (p = 0.915) and light hair color shade (p = 0.962). Our data allow us to conclude that the unknown individuals under investigation have significant genetical and phenotypical similarity with the modern Belarusian population.В ходе археологических раскопок на территории костела Божьего Тела в Несвиже были обнаружены регулярные захоронения XVII–XVIII вв. Костные останки семи неизвестных лиц подвергнуты изучению с использованием подходов генетической экспертизы и ДНК-фенотипирования. Анализ маркеров половой принадлежности показал, что останки индивидов № 1, 2 и 6 принадлежат женщинам, индивидов № 3, 4, 5 и 7 – мужчинам. В ходе исследования STR маркеров аутосомной и Y-хромосомной ДНК были получены индивидуальные профили для пяти индивидов и исключено родство первого порядка между женщиной № 1 и мужчинами № 3, 4, 5 и 7. Согласно Y-STR профилям мужчины № 3, 4, 7 относятся к гаплогруппе R1a, гаплотип индивида № 5 соответствует гаплогруппе I2, которые широко представлены на территории Восточной Европы, что с высокой долей вероятности позволяет предполагать славянское происхождение исследуемых лиц. Для установления фенотипических особенностей индивидов использовали систему HIrisPlex, генотипирование в которой позволило получить удовлетворительные результаты для женщины № 1 и мужчины № 7. Данные оценки аллельных вариантов 24 SNP системы свидетельствуют в пользу славянского типа их внешности: с высокой вероятностью женщина № 1 имела зеленые глаза, темно-русые волосы и светлый оттенок кожи; мужчина № 7 являлся светлым шатеном с голубыми глазами. Совокупность полученных данных позволяет сделать вывод, что исследуемые останки принадлежат представителям населения, генетически и фенотипически схожего с современной белорусской популяцией

СВЯЗЬ ДИФФЕРЕНЦИАЛЬНОГО ДНК-ПОЛИМОРФИЗМА ТОМАТА (SOLANUM LYCOPERSICUM L.) С ГЕТЕРОТИЧЕСКИМ ПОТЕНЦИАЛОМ ГИБРИДОВ F1

To investigate the impact of differential DNA polymorphisms of initial breeding sources on the superior F1 performance, we carried out the screening of their allelic composition and performed the genetic analysis of lines and its hybrids in the test cross design. As a result, it is shown that the overall and locus-specific heterozygosity is important for the formation of the F1 heterotic response, and the evaluation of molecular polymorphisms could be useful for the prediction of promising crosscombinations.При изучении роли дифференциального ДНК-полиморфизма исходного материала в формирование гетерозиготного преимущества гибридов F1 выполнен скрининг аллельного состава микросателлитных локусов томата. Проведен генетический анализ линий и гибридов, полученных по схеме топкросса. В результате показано, что общая и локусспецифическая гетерозиготность имеют важное значение при формировании гетеротического ответа в F1 и оценка молекулярно-генетического полиморфизма может быть полезна для предсказания перспективных комбинаций

Вариация пигментации радужки глаз белорусской популяции в связи с полиморфизмом генов HERC2 и OCA2

The human genetic phenotyping is one of the most intensely developing area of forensic genetics. Externally visible traits, including eye color, can be predicted by analyzing single nucleotide polymorphisms with a high predictive rate. We studied the polymorphisms rs12913832 and rs1800407 in the HERC2 and OCA2 genes, respectively, to evaluate its prognostic availability in relation to the iris pigmentation of the Belarusian population. For this, both eye images and DNA samples were collected from 314 individuals to analyze the key polymorphisms by the TaqMan assay. Our data confirmed a relevance of rs12913832:A>G and rs1800407:G>A in the prediction context. The highest values of the sensitivity (SE = 0.94) and the specificity (SP = 0.90) were obtained for rs12913832, demonstrating the high efficiency of this marker as a classifier of phenotypic groups. The presence of the ancestral dominant allele rs12913832-A causes a dark (brown) iris pigmentation, how- ever, the heterozygous state rs12913832:GA includes a range of mixed variants. The predictive value of rs1800407 for the genetic phenotyping is highly significant (SE = 0.98), but has a low specificity (SP = 0.14), thus rs1800407, not being an effective classifier, can be used as an auxiliary in the eye color predictive model. The analysis of a cumulative impact of the both poly- morphisms on the iris color variation shows their high prospects for the genetic phenotyping of the Belarusian population.Генетическое фенотипирование человека – новое, интенсивно развивающееся направление криминалистической генетики. Исследование генетических основ цветовой вариации глаз является одним из наиболее перспективных среди подходов, нацеленных на установление облика неизвестного индивида по характеристикам его ДНК. В данной работе проведено изучение полиморфизмов rs12913832 и rs1800407 в генах HERC2 и ОСA2 соответственно в связи с пигментацией радужки глаз белорусской популяции и дана оценка их прогностической эффективности для генетического фенотипирования. Полученные данные подтвердили значимый вклад в цветовую вариацию радужки глаз rs12913832:A>G и rs1800407:G>A. Высокие значения чувствительности (SE = 0,94) и специфичности (SP = 0,90) были получены для rs12913832, подтвердив эффективность данного маркера для использования в качестве классификатора фенотипических групп. Наличие предкового доминантного аллеля rs12913832-A обусловливает темную пигментацию радужки, однако гетерозиготное носительство rs12913832:GA включает значительный спектр смешанных вариантов. Однонуклеотидный полиморфизм rs1800407 характеризуется высокой чувствительностью (SE = 0,98), однако имеет низкое значение специфичности (SP = 0,14), следовательно, данный маркер, не являясь эффективным классификатором, может использоваться только как вспомогательный инструмент для предсказания цвета глаз. Оценка совокупного вклада изученных полиморфизмов в цветовую вариацию радужки глаз белорусской популяции показывает их высокий прогностический потенциал для генетического фенотипирования

USE OF RAPD MARKERS OPTIMIZES THE SELECTION OF SOURCE MATERIAL OF SWEET PEPPER (CAPSICUM ANNUUM L.) IN BREEDING FOR HETEROSIS

RAPD analysis of sweet pepper lines of various ecogeographical origins was made to study DNA screening efficiency for hybrid breeding. Genetic distances among parental lines were calculated. The collection was classified by UPGMA. Hybridization of polymorphic genotypes was carried out in 5 × 5 diallel cross. The combining ability of lines and the F1 heterosis effect were evaluated. Combinations with high levels of heterosis for performance traits were revealed. The contributions of additive and dominant genes to the realization of the genetic potential of parental lines were determined. Our study showed that the specific combining ability of lines of the sweet pepper collection was more important for the formation of heterosis than the general combining ability. Positive correlations between DNA marker distances of parents and heterosis degree were found for some performance traits, however, their levels were low. We plan seeking specific DNA loci that would be positively associated with hybrid performance