Hybrid Populations Research Articles

Natural hybridization reduces vulnerability to climate change

Under climate change, species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate-relevant genes. However, hybridization as a source of novel adaptive variation is typically ignored in genomic vulnerability studies. We estimated environmental niche models and genomic vulnerability for closely related species of rainbowfish (Melanotaenia spp.) across an elevational gradient in the Australian Wet Tropics. Hybrid populations between a widespread generalist and several narrow range endemic species exhibited reduced vulnerability to projected climates compared to pure narrow endemics. Overlaps between introgressed and adaptive genomic regions were consistent with a signal of adaptive introgression. Our findings highlight the often-underappreciated conservation value of hybrid populations and indicate that adaptive introgression may contribute to evolutionary rescue of species with narrow environmental ranges.

Genome-wide association and genomic prediction for resistance to southern corn rust in DH and testcross populations.

Southern corn rust (SCR), caused by Puccinia polysora Underw, is a destructive disease that can severely reduce grain yield in maize (Zea mays L.). Owing to P. polysora being multi-racial, it is very important to explore more resistance genes and develop more efficient selection approaches in maize breeding programs. Here, four Doubled Haploid (DH) populations with 384 accessions originated from selected parents and their 903 testcross hybrids were used to perform genome-wide association (GWAS). Three GWAS processes included the additive model in the DH panel, additive and dominant models in the hybrid panel. As a result, five loci were detected on chromosomes 1, 7, 8, 8, and 10, with P-values ranging from 4.83×10-7 to 2.46×10-41. In all association analyses, a highly significant locus on chromosome 10 was detected, which was tight chained with the known SCR resistance gene RPPC and RPPK. Genomic prediction (GP), has been proven to be effective in plant breeding. In our study, several models were performed to explore predictive ability in hybrid populations for SCR resistance, including extended GBLUP with different genetic matrices, maker based prediction models, and mixed models with QTL as fixed factors. For GBLUP models, the prediction accuracies ranged from 0.56-0.60. Compared with traditional prediction only with additive effect, prediction ability was significantly improved by adding additive-by-additive effect (P-value< 0.05). For maker based models, the accuracy of BayesA and BayesB was 0.65, 8% higher than other models (i.e., RRBLUP, BRR, BL, BayesC). Finally, by adding QTL into the mixed linear prediction model, the accuracy can be further improved to 0.67, especially for the G_A model, the prediction performance can be increased by 11.67%. The prediction accuracy of the BayesB model can be further improved significantly by adding QTL information (P-value< 0.05). This study will provide important valuable information for understanding the genetic architecture and the application of GP for SCR in maize breeding.

The potential effects of chlorophyll-deficient mutation and tree_age on the accumulation of amino acid components in tea plants

Albino tea has been receiving growing attention on the tea market due to its attractive appearance and fresh taste, mainly caused by high amino acid contents. Here, variations in the contents of five free amino acids in relation to pigment contents and tree age in two hybrid populations‘Longjin 43′(♀) × ‘Baijiguan’(♂) and ‘Longjin 43′(♀) בHuangjinya’(♂) with 334 first filial generation individuals including chlorophyll-deficient and normal tea plants were investigated. The data showed that the contents of main amino acids in all filial generation gradually decreased as plant age increased. Principal component analysis indicated that the amino acid content of individual plant tended to be stable with the growth of plants. Correlation analysis clarified that several main amino acids were significantly negatively correlated with chlorophyll a, chlorophyll b and carotenoid contents. Our results showed that the accumulation of amino acids in tea plant was closely related to leaf color variation and the tree age during growing period.

Determination of genomic regions related citrus chlorotic dwarf disease in clementine mandarin × Minneola tangelo hybrid population by QTL analysis

Determination of genomic regions related citrus chlorotic dwarf disease in clementine mandarin × Minneola tangelo hybrid population by QTL analysis

Modeling the influence of phenotypic plasticity on maize hybrid performance

Phenotypic plasticity, the ability of an individual to alter its phenotype in response to changes in the environment, has been proposed as a target for breeding crop varieties with high environmental fitness. Here, we used phenotypic and genotypic data from multiple maize (Zea mays L.) populations to mathematically model phenotypic plasticity in response to the environment (PPRE) in inbred and hybrid lines. PPRE can be simply described by a linear model in which the two main parameters, intercept a and slope b, reflect two classes of genes responsive to endogenous (class A) and exogenous (class B) signals that coordinate plant development. Together, class A and class B genes contribute to the phenotypic plasticity of an individual in response to the environment. We also made connections between phenotypic plasticity and hybrid performance or general combining ability (GCA) of yield using 30 F1 hybrid populations generated by crossing the same maternal line with 30 paternal lines from different maize heterotic groups. We show that the parameters a and b from two given parental lines must be concordant to reach an ideal GCA of F1 yield. We hypothesize that coordinated regulation of the two classes of genes in the F1 hybrid genome is the basis for high GCA. Based on this theory, we built a series of predictive models to evaluate GCA in silico between parental lines of different heterotic groups.

Marker-Assisted Recurrent Selection for Pyramiding Leaf Rust and Coffee Berry Disease Resistance Alleles in Coffea arabica L.

In this study, marker-assisted recurrent selection was evaluated for pyramiding resistance gene alleles against coffee leaf rust (CLR) and coffee berry diseases (CBD) in Coffea arabica. A total of 144 genotypes corresponding to 12 hybrid populations from crosses between eight parent plants with desired morphological and agronomic traits were evaluated. Molecular data were used for cross-certification, diversity study and resistance allele marker-assisted selection (MAS) against the causal agent of coffee leaf rust (Hemileia vastatrix) and coffee berry disease (Colletotrichum kahawae). In addition, nine morphological and agronomic traits were evaluated to determine the components of variance, select superior hybrids, and estimate genetic gain. From the genotypes evaluated, 134 were confirmed as hybrids. The genetic diversity between and within populations was 75.5% and 24.5%, respectively, and the cluster analysis revealed three primary groups. Pyramiding of CLR and CBD resistance genes was conducted in 11 genotypes using MAS. A selection intensity of 30% resulted in a gain of over 50% compared to the original population. Selected hybrids with increased gain also showed greater genetic divergence in addition to the pyramided resistance alleles. The strategies used were, therefore, efficient to select superior coffee hybrids for recurrent selection programs and could be used as a source of resistance in various crosses.

Сollection of melon crops: identification of homologous series in hereditary variability

The law of homologous series in variation has important significance for disclosing the potential hereditary variability in plants. The use of the law in studies of cucurbit cropcollections, hybrid populations, mutants, and breeding lines made it possible to discover valuable and previously unknown forms of watermelon, muskmelon and different squash species for their use in practical breeding. For example, these are bushy and short vine forms for breeding cultivars suitable for mechanized cultivation. This work resulted in creating cultivars of bushy watermelon ‘Svaytoslav’, short vine watermelon ‘Podarok Solntsa’, bushy Cucurbita pepo L. ‘Kustovaya oranzhevaya’ and Cucurbita maxima Duch. ‘Kustovaya Zolotaya’, ‘Malyshka’, and ‘Matrieschka’, short vine Cucurbita maxima Duch. ‘Lechebnaya’ and Cucurbita moschata Duch. ex Poir ‘Mariya’, and also of a short vine muskmelon ‘Stanislava’. The mentioned cultivars have been included in the State Register of Selection Achievements. Watermelon genetic marker lines with the nonlobed (entire) leaf (TsL), namely TsL 656, TsL 662, TsL 784, TsL 752, have been identified and used for crerating entire leaf cultivars ‘Blagodatnyi’, ‘Lubimchik’, and ‘Krasavchik’. A watermelon cultivar ‘Surpriz’ with high quality, delicately colored bright yellow flesh, and cultivar ‘Solyaris’ with fruits combining yellow color of rind with yellow flesh, have been created for cultivation by amateur gardeners. Of interest is an ornamental form of watermelon with yellow-green mosaic leaf and bright yellow fruits (the yellowgreen bushy line) ZhZKL 870, as well as the yellow-green muskmelon line ZhZL 487 and yellow-green pumpkin (Cucurbita maxima) line ZhZL 692. Bushy lines KL 648, KL 652 and short vine KPL 648, KPL 652 of pumpkin (Cucurbita moschata) have been created. Improved female lines (ZhL) of muskmelon (ZhL 415, ZhL 421, ZhL 423, and ZhL 427) have been identified for heterosis breeding. It follows from the above that the law in question found practical application in breeding cucurbit crops.

Creation of new germplasm resources, development of SSR markers, and screening of monoterpene synthases in thyme

BackgroundThyme derived essential oil and its components have numerous applications in pharmaceutical, food, and cosmetic industries, owing to their antibacterial, antifungal, and antiviral properties. To obtain thyme essential oil with different terpene composition, we developed new germplasm resources using the conventional hybridization approach.ResultsPhenotypic characteristics, including essential oil yield and composition, glandular trichome density, plant type, and fertility, of three wild Chinese and seven European thyme species were evaluated. Male-sterile and male-fertile thyme species were crossed in different combinations, and two F1 populations derived from Thymus longicaulis (Tl) × T. vulgaris ‘Fragrantissimus’ (Tvf) and T. vulgaris ‘Elsbeth’ (Tve) × T. quinquecostatus (Tq) crosses were selected, with essential oil yield and terpene content as the main breeding goals. Simultaneously, simple sequence repeat (SSR) primers were developed based on the whole-genome sequence of T. quinquecostatus to authenticate the F1 hybrids. A total of 300 primer pairs were selected, and polymerase chain reaction (PCR) was carried out on the parents of the two hybrid populations (Tl, Tvf, Tve, and Tq). Based on the chemotype of the parents and their F1 progenies, we examined the expression of genes encoding two γ-terpinene synthases, one α-terpineol synthase, and maybe one geraniol synthase in all genotypes by quantitative real-time PCR (qRT-PCR).ConclusionWe used hybridization to create new germplasm resources of thyme, developed SSR markers based on the whole-genome sequence of T. quinquecostatus, and screened the expression of monoterpene synthase genes in thyme. The results of this study provide a strong foundation for the creation of new germplasm resources, construction of the genetic linkage maps, and identification of quantitative trait loci (QTLs), and help gain insight into the mechanism of monoterpenoids biosynthesis in thyme.

Genetic parameters and response to selection for thermal tolerance, summer survival and growth in hybrid oyster (Crassostrea gigas ♀ × C. angulata ♂)

The Pacific oyster Crassostrea gigas is the most commonly farmed mollusks worldwide, while its production has been hindered by massive mortalities linked to high temperatures. Selective breeding focusing on thermal tolerance is an attractive option for reducing the impact of massive mortalities, but the genetic basis underlying this trait is currently unknown. Hybridization between C. gigas and C. angulata was conducted and followed by one generation of family selection for thermal tolerance. The genetic parameters for thermal resistance, summer survival and growth and selection response were investigated by using 50 full-sibling families. The mean survival of all families ranged from 30.2 to 69.5%, reflecting the large variation of thermal tolerance in the hybrid population. The estimates of heritability for thermal tolerance were low to moderate, ranging from 0.19 ± 0.03 to 0.27 ± 0.05, confirmed that there is genetic basis for thermal tolerance. The phenotypic (r = 0.537, P &lt; 0.01) and genetic correlations (r = 0.546, P &lt; 0.01) between thermal tolerance and summer survival were positive and significant, while the phenotypic and genetic correlations between growth and survival (including thermal tolerance and summer survival) were positive but low (P &gt; 0.05). High response to selection (ΔG = 36.33%) was observed after one generation of selection for thermal tolerance, and there was also corresponding response (ΔG = 14.46%) for summer survival. These results demonstrated that genetic selection to improve summer survival of oyster may be facilitated by selecting highly heat-tolerant lines.

SNPs Detection and Genetic Analysis of Chionanthus retusus via Genotyping-by-Sequencing

Abstract Chionanthus retusus is one of the well-known ornamental trees in East Asia and America. Not only its value in the market but also had the potential as a source for producing antioxidant. However, due to uncontrolled exploitation, the number of wild C. retusus in China is decreasing rapidly. The genetic study of C. retusus is limited. In order to investigate the genetic diversity and the distribution of C. retusus in China, 47 samples from 8 different provinces have been sequenced via restriction site-associated DNA sequencing (RAD-seq). Totally, 31, 402 high-quality single nucleotide polymorphisms (SNP) were obtained. According to the phylogenetic tree and the principal component analysis, the samples were divided into four populations, including 3 major populations and 1 hybrid population. Population1 were the samples from Jiangsu and Yunnan province and the Population2 were mainly from northern and northeast of China including Liaoning and Hubei province, while the Population4 were from Shandong and Henan province, which were in central China. As the admixture showed, the population3 were the offspring of the other 3 populations by hybridization. The mean heterozygosity of Chinese Fringe tree from different province is 0.42 %, with the highest heterozygosity, which is as high as 0.63 %, from Jiangsu province and the lowest heterozygosity, which is only 0.19, from Henan province. This is the first report about the genetic diversity and relationship of Chionanthus retusus, which will provide value information for further genetic study, genomic study, conservation and breeding.

Genome-wide association analysis for grain moisture content and dehydration rate on maize hybrids.

The online version contains supplementary material available at 10.1007/s11032-022-01349-x.

Evolution of a hybrid zone of two willow species (Salix L.) in the European Alps analyzed by RAD-seq and morphometrics.

Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise in mountain systems as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. Willows are a large genus of woody plants with an immense capability of interspecific crossing. In this study, the sympatric area of two diploid sister species, S.foetida and S.waldsteiniana in the eastern European Alps, was investigated to study the genomic structure of populations within and outside their contact zone and to analyze congruence of morphological phenotypes with genetic data. Eleven populations of the two species were sampled across the Alps and examined using phylogenetic network and population genetic structure analyses of RAD Seq data and morphometric analyses of leaves. The results showed that a homoploid hybrid zone between the two species was established within their sympatric area. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to not only one of the parental species but also one hybrid population forming a separate lineage. The lack of F1 hybrids indicated a long-term persistence of the hybrid populations. Insignificant isolation by distance suggests that gene flow can act over large geographical scales. Morphometric characteristics of hybrids supported the molecular data and clearly separated populations of the parental species, but showed intermediacy in the hybrid zone populations with a bias toward S.waldsteiniana. The homoploid hybrid zone might have been established via secondary contact hybridization, and its establishment was fostered by the low genetic divergence of parental species and a lack of strong intrinsic crossing barriers. Incomplete ecological separation and the ability of long-distance dispersal of willows could have contributed to the spatial expansion of the hybrid zone.

Optimization of the breeding process of lodging-resistant varieties of spring triticale

During the field and laboratory studies, selection samples of spring hexaploid triticale were studied according to breeding valuable traits and physical and mechanical properties of the stem. As a result of the research, an information database was created, which contains information on the study of samples according to economically valuable characteristics, product quality, a set of characteristics of biometric and physical and mechanical properties of the tissue of spring triticale stems. The set of data contained in the database, can be used in the selection of parent pairs for hybridization, selection of valuable genotypes from hybrid populations, in the breeding of new lodging-resistant varieties.

Creation of selected items with high fiber yield and length based on cotton composite hybrids

The wide range of possibilities of using double, complex and double crossing methods in cotton has been studied in selection research. As a result of the use of complex hybridization, valuable traits of varieties of different genetic origin can be collected in a single genotype in a short period of time. Because in the hybrids created on the basis of complex cross-breeding, the variability of quantitative characters is manifested on a large scale, and the possibility of extensive selection appears in these hybrid populations. It is important to use various breeding methods in cotton selection, which are widely used in other agricultural crops. As a result of transgressive variation occurring in composite hybridization in cotton, the increase in the possibility of isolating recombinants, which are the source of new genetic variations, which gives the opportunity to create new varieties with a positive set of valuable economic characters in a short time, has been confirmed in the selection of other crops. In the article, it is stated that the correct selection of parental pairs and the use of composite hybridization method are important for the improvement of fiber yield and fiber length in the creation of new varieties of cotton. In particular, the effectiveness of using T-3377, T-3378, T-3379 varieties, created on the basis of composite hybridization, in achieving positive results in terms of fiber yield and fiber length was highlighted.

Heterosis and maternal effect on parameters related to productivity of 25 cross populations between five strains of common carp

Heterosis is a comparison of the performance of hybrid fish compared to their parents. Positive heterosis indicates the hybrid performance is better than the parents' average. The maternal-effect in the hybridization process causes the heterosis not to be the only consideration in the formation of hybrid fish. The primary goal of this study was to estimate heterosis and conduct an evaluation of the maternal effect, especially on parameters related to the productivity of cross-population between five common carp strains in Indonesia, specifically Majalaya (MJ), Rajadanu (Rj), Sutisna (St), Wildan (Wd), and Sinyonya (Sy). The grow out of the hybrid and inbred line populations was carried out in 25 net cages, measuring 5x5 meters, for 90 days. The fish rearing was conducted with three replications. The results showed that the highest heterosis for harvested biomass as the productivity parameter was achieved in the five crosses, that is, Rj &gt;&lt; St, Rj &gt;&lt; Mj, Mj &gt;&lt; St, Sy &gt;&lt; Stand Sy &gt;&lt; Mj. The common carp strain with the highest maternal effect on the productivity parameter is the Majalaya strain. Female selection in the Majalaya strain affects the performance in terms of phenotypic characteristic of the cultured hybrid common carp

Genetic diversity and paternity analysis of Mytilaria laosensis hybrids using microsatellite markers provide insight into the breeding system

Mytilaria laosensis is an important evergreen broadleaf tree species in Southeast Asia and can provide excellent raw materials for pulp and fiberboard industrial production due to its fast growth and desirable wood properties. It produces hundreds of hermaphrodite flowers in a single inflorescence and controlled pollination through emasculation is difficult. In this study, we adopted hand-assisted pollination to investigate the seed set ratio and hybrid efficiency. A total of 65 cross combinations including 723 inflorescences were performed by using five female and eight male trees. The fruit-set rate varied greatly from 6.67% to 84.62% among different groups with an average of 23.68%. Moreover, new microsatellite markers were developed through transcriptome sequencing and ten polymorphic markers were screened out to examine the genetic variation and hybrid purity of 742 progeny. An average of 14.7 alleles was detected per locus. The parent population showed the highest expected heterozygosity of 0.77, while other hybrid populations exhibited different heterozygosity values from 0.46 to 0.71. Both principal coordinate analysis and phylogenetic tree revealed that these groups could be divided into five clusters and each cluster represented progeny which shared the same female parent. Paternity test showed that 18 offspring were sired by the designated pollen parents, while all other offspring were all heterozygous with pollens from non-target father. The results implied that outcrossing might be the predominant breeding system and self-incompatibility might exist in M. laosensis . This study provides useful reference for molecular-assisted hybrid breeding research and a practicable approach for new cultivar development in tree species. • The fruit-set rate varied greatly in different cross combinations of M. laosensis . • Ten highly efficient SSR markers were developed through transcriptome sequencing. • High genetic diversity level was detected among 52 hybrid groups. • The 18 offspring were sired by the designated parents and others were all heterozygous. • Self-incompatibility might exist in M. laosensis.

Introduction of breeding samples of meadow clover according to economically valuable characteristics using modern breeding methods

The paper presents the results of research on the formation of complex hybrid populations, an assessment of the collection samples of clover on a complex of economically valuable traits for the creation of forage varieties. The basis for the study were promising plants that weresown in a wide row and individually in a row. By negative selection, weak and underdeveloped plants were mowed down. It`s been noticed that there was the direct dependence of clover seeds` creation from the weather conditions. The collection samples of meadow clover`s assessment was given according to the complex of economically valuable features for the creation of the hay –pasture type varieties. The best samples are allocated for the yield of the green mass, the plants` height. The initial material was obtained on the signs of adaptability, yield of green mass, foliage and seed productivity. Promising clover samples were selected for high seed productivity, reaching more than 60 %. Similarly, in accordance with the vertical zonality of the natural habitats of wild introducers, the protein content in plant samples also increases. In terms of fodder yield, the maximum indicators were noted in the varieties Farn, Ustodlivy (Belorussian selection), Orlik (All-Russian Scientific Research Institute of Legumes and Millet Crops), complex hybrid populations that exceeded the standard – the Daryal variety by 12-25%. According to seed, Nart varieties were distinguished. Synthetic populations Syn 305-03, Syn 274-94 (selection SKNIIGPSH VNC RAS), FM-143(VNII kordov), Dargavsky, (wild specimen of RSO – Alanya).

Biometric characters and their correlation in F5 hybrid populations of durum spring wheat breeding of Umansky NUH

Biometric characters and their correlation in F5 hybrid populations of durum spring wheat breeding of Umansky NUH

The influence of genotype and year conditions on the transgressive variability of stem length in popu-lations of the second generation of soft winter wheat

In 2019–2020, in the conditions of the experimental field of the Bila Tserkva National Agrarian University, populations of F2 hybrids, created by crossing soft winter wheat varieties that differ in the duration of the growing season, were studied. The aim of the work was to establish the degree and frequency of transgressions in the length of the main stem depending on the meteorological conditions of the year and the parental forms selected for hybridization, and to select selectively valuable recombinants for further research. In 2019, in 40 out of 42 F2 populations, only a positive degree of transgression was established in terms of the length of the main stem, from 2.5 % (Myronivsk early/Kolchuga) to 53.8 % (Zolotokolosa/Shchedra nyva). With the use of maternal cytoplasm of early ripening varieties in four populations, all plants exceeded the extreme maximum values of the parents, and with the hybridization of mid-early, mid-ripening, mid-late varieties, 13 such combinations were studied. In the conditions of 2020, positive transgressive recombinants were isolated only in six out of 20 populations based on hybridization with the maternal form of early-ripening varieties, and negative ones – in nine. Negative transgressive recombinants were selected in 13 of 21 populations created by crossing mid-early, mid-maturing, mid-late varieties. At the same time, no positive transgressions were found. The selection of parental pairs differing in precociousness before hybridization expands morphogenesis in F2 populations of soft winter wheat and promotes the selection of both positive and negative transgressive recombinants by the length of the main stem. A significant influence of meteorological conditions and initial forms of hybridization on the formation of stem length and the manifestation of extreme maximum and minimum values in populations of the second generation of soft winter wheat was established. The use of early-ripening cytoplasm in hybridization has a greater effect on the positive transgressive variability of the length of the main stem in F2 populations compared to medium-early, medium-maturing and medium-late maternal forms. Key words: degree and frequency of transgressions, soft winter wheat, maturity groups, parent forms, main stem length, F2 populations.

Phenotypic and Genetic Variation in Morphophysiological Traits in Huanglongbing-Affected Mandarin Hybrid Populations

Huanglongbing (HLB) caused by 'Candidatus Liberibacter asiaticus' (CLas) is the most costly disease for the global citrus industry. Currently, no effective tools have been found to control HLB. Most commercial citrus varieties are susceptible to HLB, though some citrus hybrid cultivars have reduced sensitivity to the disease. Citrus breeding populations contain a large diversity of germplasm, with thousands of unique genotypes exhibiting a broad range of phenotypes. Understanding phenotypic variation and genetic inheritance in HLB-affected mandarin hybrid populations are crucial for breeding tolerant citrus varieties. In this study, we assessed 448 diverse mandarin hybrids coming from 30 crosses, and 45 additional accessions. For HLB tolerance, we measured HLB severity visual score and CLas titers by qPCR. We also measured seven morphophysiological traits indirectly related to HLB tolerance with leaf area index (LAI), leaf area (LA), leaf mass per area (LMA), photosystem II parameters (Fv/Fo, Fv/Fm), and photochemical performance index (PIabs). By estimating the genetic variation in five half-sib families, we estimated the heritability of phenotypic traits and found a significant genetic effect on HLB visual score and photosynthesis parameters, which indicates opportunities for the genetic improvement of HLB tolerance. In addition, although it is easy to identify infected trees based on HLB symptomatic leaves, visually phenotyping whole trees can be difficult and inconsistent due to the interpersonal subjectivity of characterization. We investigated their relationships and found that LAI was highly correlated with HLB score, with correlation coefficients of r = 0.70 and r = 0.77 for the whole population and five half-sib families, respectively. Photochemical parameters showed significant correlation with HLB severity and responded differentially with the side of the canopy. Our study suggests that LAI and photochemical parameters could be used as a rapid and cost-effective method to evaluate HLB tolerance and inheritance in citrus breeding programs.