F1 Hybrid Population Research Articles

Active avoidance learning in rats with different audiogenic epilepsy proneness

The success of the formation of the conditioned reflex reaction of two-way avoidance in the shuttle chamber in rats of 3 strains was evaluated. These were rats predisposed to audiogenic epilepsy – the Krushinsky-Molodkina strain rats (KM), "4" strain (selected from a population of F2 hybrids of the KM strain and sound-insensitive Wistars) and rats of "0" strain, selected for the absence of audiogenic epilepsy from the same population (i. e. these strains, diametrically different in audiogenic epilepsy proneness, possessing a similar genetic background). Experiments have shown significantly more successful assimilation of this skill in rats of the "0" strain.

The inheritance pattern for the dwarf phenotype in hybrids from crosses among sunflower lines differing in alleles of the Rht1 locus

Background. Sunflower seed production is based on utilization of the heterosis effect, manifesting itself in improving both yield and plant height in hybrids. Short-stemmed lines need to be used to develop commercial hybrids with an optimum height. Molecular bases of the trait manifestation in the dwarf lines from VIR’s sunflower genetic collection have not yet been studied. Materials and methods. The material included 27 short-stemmed and 10 tall sunflower lines from VIR’s genetic collection, as well as the F1 and F2 hybrid generations derived from crossing the tall (VIR 340) and dwarf (VIR 171) genotypes. The parental lines and hybrids were phenotyped for plant height, leaf number, and internode length. Genotyping for the Rht1 locus (HaDella1 candidate gene), encoding the negative regulator of the gibberellin response, the DELLA protein, was performed using the developed CAPS marker. Results. The average plant height in the VIR 340 line over a three-year study was 162 cm, the number of leaves 29, and the internode length 6 cm. The VIR 171 line demonstrated the plant height of 66 cm, leaf number of 24, and internode length of 2.8 cm. The F1 hybrids were uniform, with the height of 180–190 cm, that indicated the dominance of the long stem trait. Analyzing the segregation in the F2 hybrid generation led to an assumption admitting the digenic control of the dwarf phenotype in the VIR 171 line. The CAPS marker G-D-1/ Bmt I was developed to identify a missense mutation T>C in the first exon of the HaDella1 gene, which results in the substitution of leucine with proline in the DELLA motif. Using the marker, the mutant Rht1 allele was identified in the VIR 171 and VIR 434 dwarf lines, similar in their origin and phenotype. The results of validation in the F2 hybrid population (VIR 340 × VIR 171) confirmed the efficiency of the G-D-1 / Bmt I marker for selecting dwarf genotypes homozygous for the Rht1 mutant allele.

MdNAC5: a key regulator of fructose accumulation in apple fruit.

The sweetness of apple fruit is a key factor in the improvement of apple varieties, with fructose being the sweetest of the soluble sugars, playing a crucial role in determining the overall sweetness of the apple. Therefore, uncovering the key genes controlling fructose accumulation and deciphering the regulatory mechanisms of fructose are vitally important for the improvement of apple varieties. In this study, through BSA-seq and transcriptome analysis of the 'Changfu 2' × 'Golden Delicious' F1 hybrid population, MdNAC5 was identified as a key regulatory gene for fructose content. MdNAC5 was shown to significantly influence fructose accumulation in both apples and tomatoes. Furthermore, we conducted a detailed identification of sugar transporters and metabolic enzymes in apples, discovering that MdNAC5 can enhance fructose accumulation in vacuoles and the conversion of sucrose to fructose by binding to and activating the promoters of the vacuolar sugar transporter MdTST2 and the neutral invertase MdNINV6. Additionally, MdNAC5 regulated the MdEIN3.4-MdSWEET15a module, strengthening the unloading of sucrose in the phloem of the fruit. Our results reveal a new mechanism by which MdNAC5 regulates fructose accumulation in apples and provide theoretical foundations for improving apple sweetness through genetic modification.

Authenticity Identification of F1 Hybrid Offspring and Analysis of Genetic Diversity in Pineapple

Breeding is an effective method for the varietal development of pineapple. However, due to open pollination, it is necessary to conduct authentic identification of the hybrid offspring. In this study, we identified the authenticity of offspring and analyzed the genetic diversity within the offspring F1 hybrids resulting from crosses between ‘Josapine’ and ‘MD2’ by single nucleotide polymorphism (SNP) markers. From the resequencing data, 26 homozygous loci that differentiate between the parents have been identified. Then, genotyping was performed on both the parents and 36 offspring to select SNP markers that are suitable for authentic identification. The genotyping results revealed that 2 sets of SNP primers, namely SNP4010 and SNP22550, successfully identified 395 authentic hybrids out of 451 hybrid offspring. We randomly selected two true hybrids and four pseudohybrids for sequencing validation, and the results have shown that two true hybrids had double peaks with A/G, while pseudohybrids had single peaks with base A or G. Further study showed that the identification based on SNP molecular markers remained consistent with the morphological identification results in the field, with a true hybridization rate of 87.58%. K-means clustering and UPGMA tree analysis revealed that the hybrid offspring could be categorized into two groups. Among them, 68.5% of offspring aggregated with MD2, while 31.95% were grouped with Josapine. The successful application of SNP marker to identify pineapple F1 hybrid populations provides a theoretical foundation and practical reference for the future development of rapid SNP marker-based methods for pineapple hybrid authenticity and purity testing.

Genome-wide analysis with additive and epistasis effects reveals growth-related loci and candidate genes in hybrid Argopecten scallops

The first filial (F1) generation from the successful hybridization of bay scallops (Argopecten irradians) and Peruvian scallops (A. purpuratus) exhibits significant heterosis, playing a crucial role in enhancing the germplasm and increasing yields of the scallops. However, there is significant variation in the growth traits of the F1 hybrid population, and there is little information concerning its hereditary basis. To unravel the heterosis mechanism and identify key loci and genes contributing to superhybrids, genome-wide association study (GWAS) with additive and epistasis models were conducted for six growth-related traits in the F1 hybrid scallop population in this study. In total, 18,789,547 single nucleotide polymorphisms (SNPs) were identified after filtering from 198 hybrid individuals, comprising 63.5% of maternal loci and 36.5% of paternal loci. The additive model revealed 2768 associated SNPs and 14 candidate genes, with most of the loci associated with the body mass traits. The additive-additive epistatic model identified 133,094 SNP interaction pairs and 20 candidate gene pairs with exon region SNPs, which were predominantly associated with shell morphology traits. Almost all the SNP pairs associated with body mass traits were maternal-maternal interactions, but the shell morphology traits had the most maternal-paternal and maternal-maternal interactions, suggesting that body mass traits might be affected mainly by maternal effects and that parental interaction effects mainly contributed to the shell size of the hybrid scallops. Both in the shell morphology and the body mass traits, multiple loci participate in epistasis, interacting with more than one locus and forming high-order epistatic interactions, which could be critical factors contributing to the heterosis observed in hybrid scallops. The identified associated loci and candidate genes not only constitute valuable resources for the molecular breeding of hybrid scallops, contributing to the improvement of growth-related traits, but also revealed mechanisms underlying heterosis in aquatic species, providing insights into the advantages of heterosis and paving the way for future research on hybridization in aquatic organisms.

Comparison and Genetic Variation Analysis of Important Fruit Traits in Jujube F1 Hybrids by Different Male Parents

The research on the genetic predisposition of key quality traits of fruit in jujube hybrid populations is a fundamental and crucial aspect in the field of jujube genetic breeding. In this study, the jujube hybridization experiments were conducted with the same female parent and different male parents since 2015, and a total of 238 strains were created in two F1 hybrid populations. The genetic variation of fruit external traits and intrinsic quality was analyzed and compared after the hybrid offspring results were stable in 2022. This study can provide a theoretical basis for selecting hybrid-breeding parents, predicting offspring traits, and innovating excellent germplasm resources by investigating the impact of different male parental configurations on the genetic variation of fruit traits in jujube hybrid offspring and identifying superior germplasm resources. The results showed that the inheritance of fruit shape, fruit size, and fruit-intrinsic nutrition-quality traits were quantitative traits controlled by multiple genes, and the offspring populations conformed to normal distribution or partial normal distribution. The six traits of fruit shape in offspring populations exhibited a segregation from their parents. The coefficients of variation of fruit size and intrinsic nutrition quality values ranged from 6.94% to 35.34%. Five intrinsic nutrition-quality traits exhibited significant separation at the super-parental level. This result indicated a rich genetic diversity in offspring traits in two hybrids offsprings. The fruit shape, fruit size, and titratable acidity of jujube hybrid offspring were mainly influenced by the male parent. It was found that the correlation between the single-fruit weight, length, and diameter, as well as the correlation between the fruit length and fruit transverse diameter, was very stable and significantly positive through the correlation analysis. More attention should be paid to fruit length when studying fruit shape, as a significant correlation was found between fruit length and fruit shape index. Finally, 10 superior hybrids were founded and selected as breeding materials for further breeding. Therefore, this study provides a theoretical basis for the early selection of hybrid breeding and the development and application of jujube germplasm resources.

Localization of S-Locus-Related Self-Incompatibility in Lycium barbarum Based on BSA Analysis

The recognition of pollen and pistil in the self-incompatibility process is generally determined by the interaction between the pollen S gene and pistil S gene located at the S locus. However, the regulatory mechanism of self-incompatibility in goji remains unknown. In this study, we used the self-compatible strain ‘13–19’ and self-incompatible strain ‘xin9’ from Ningxia as parents to create an F1 hybrid population. Reciprocal cross-pollination was performed within the same plant to evaluate the self-compatibility of the parents and F1 progeny. The parents and progeny were subjected to whole-genome resequencing, and mixed pools of DNA were constructed using 30 self-compatible and 30 self-incompatible individuals. Association analysis using the SNP-index method and Euclidean distance was employed to identify the key candidate region of the S locus. The candidate region was further annotated using the Swiss-Prot database to identify genes within the region. Additionally, transcriptome sequencing data from different organs/tissues, as well as from pistils of self-compatible and self-incompatible strains at control (0 h), short (0.5 h), medium (8 h), and long (48 h) time points after self-pollination and cross-pollination, were analyzed to assess differential gene expression and screen for self-compatibility-related loci. Specific primers were designed for PCR amplification to determine the S-RNase genotypes of the extreme parents. The results revealed that the S locus in goji is located within a 32.2 Mb region on chromosome 2 that contains a total of 108 annotated genes. Differential expression analysis showed that ten genes, including Lba02g01064, were specifically expressed in stamens, with four of them annotated as F-box genes, potentially serving as determinants of self-compatibility in stamens. Lba02g01102 was exclusively expressed in pistils and annotated as an S-RNase gene, likely involved in self-compatibility. The expression of Lba02g01102 in pistils decreased after self-pollination and cross-pollination. Six candidate genes exhibited significant changes after self-pollination and cross-pollination. Both parents and progeny carried two S-RNase alleles, and the S-RNase genotypes showed a significant correlation with self-compatibility, with the self-compatible progeny containing the S8-RNase allele. The identification of the S locus in goji provides molecular markers for future marker-assisted breeding and offers genetic resources for studying the mechanism of self-incompatibility in goji, thus contributing to the improvement of goji varieties.

Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population.

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.

Phenotypic Variation in Flower Color and Morphology in the Gerbera (Gerbera hybrida) F1 Hybrid Population and Their Association with EST-SSR Markers.

Gerbera (Gerbera hybrida) is a widely cultivated ornamental plant. However, its genetic improvement is limited by the lack of genetic analysis and molecular markers for traits. In this study, we analyzed the phenotypic and genotypic variation of 140 F1 progeny from two gerbera varieties with different flower types and colors. We evaluated the flower's morphology, color, and pigment content of the F1 population and performed cluster principal component analysis (PCA) and correlation analysis. The results showed that the main ornamental traits of the hybrid progeny varied greatly. The segregation ratios of single and double flowers and ligulate and split ray florets were both 1:1. The flower colors of the F1 progeny were mainly red and purple-red, similar to the male parent's color. Furthermore, we conducted a genetic analysis of the hybrid progeny using EST-SSR markers and performed association analysis with phenotypic traits. We identified 2, 2, 3, 1, and 2 loci to be associated with peduncle length (PL), ray floret length (RFL), and outer ray floret; the level of apex relative to the top of involucre (LAI); outer corolla lips (OCL); and the b* of ray floret color, respectively. Our results reveal the genetic patterns of important ornamental traits and provide a theoretical basis and practical tools for gerbera genetic breeding.

Inheritance of valuable productivity traits of hybrid combinations of local and foreign oat varieties in the conditions of the Trans-Ural region

The results of studying the character of inheritance of valuable traits of the first-generation hybrids obtained from crossing foreign and domestic varieties of oats in the conditions of the Northern Trans-Urals are presented. The experiment was conducted on the experimental field of the Scientific Research Institute of Agriculture for Northern Trans-Ural Region in 2019 and 2020. The object of the study were 18 F1 hybrid populations and 6 parent varieties: Talisman, Otrada, Foma, Sang, Solidor and Ensiler. Productivity elements were evaluated according to the methodology of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources. B.A. Dospekhov's methodology was used for statistical data processing. Inheritance of phenotypic traits was determined according to G.M. Beil and R.E. Atkins. Analysis of the yield structure elements demonstrated the lack of advantage of foreign selection varieties over the genotypes obtained in the Northern Trans-Urals. It has been established that the Otrada variety is not inferior to Sang, Solidor and Ensiler varieties in terms of panicle ear grain content and the thousand-kernel weight, and Foma is superior to them. It has been determined that crosses between the varieties of local and foreign selection have a high percentage of success (42–68%), which makes them promising in the breeding process. It has been revealed that 50% of hybrid combinations are characterized by depression in the trait "plant height" – the degree of phenotypic dominance in this case varies from –22.2 to –3.1 units. Crossing of Foma with foreign varieties ensured overdominance in the panicle height, its grain content and the thousand-kernel weight. According to the degree of phenotypic dominance of the productivity elements, the following promising hybrid combinations have been identified: Ensiler × Otrada, Sang × Otrada, Foma × Sang. In the above combinations, selection of high-yielding genotypes can be carried out from the second generation onwards. It is recommended to select promising lines among hybrid combinations, where one of the parental forms is the Foma variety, in the later generations. Hybrids of the first generation obtained from crossing the Talisman variety with Ensiler, Sang and Solidor varieties have no advantages over the parental forms and are unpromising for the breeding process.

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution.

The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.

Genomic mechanisms and consequences of diverse postzygotic barriers between monkeyflower species.

The evolution of genomic incompatibilities causing postzygotic barriers to hybridization is a key step in species divergence. Incompatibilities take two general forms - structural divergence between chromosomes leading to severe hybrid sterility in F1 hybrids and epistatic interactions between genes causing reduced fitness of hybrid gametes or zygotes (Dobzhansky-Muller incompatibilities). Despite substantial recent progress in understanding the molecular mechanisms and evolutionary origins of both types of incompatibility, how each behaves across multiple generations of hybridization remains relatively unexplored. Here, we use genetic mapping in F2 and RIL hybrid populations between the phenotypically divergent but naturally hybridizing monkeyflowers Mimulus cardinalis and M. parishii to characterize the genetic basis of hybrid incompatibility and examine its changing effects over multiple generations of experimental hybridization. In F2s, we found severe hybrid pollen inviability (< 50% reduction vs. parental genotypes) and pseudolinkage caused by a reciprocal translocation between Chromosomes 6 and 7 in the parental species. RILs retained excess heterozygosity around the translocation breakpoints, which caused substantial pollen inviability when interstitial crossovers had not created compatible heterokaryotypic configurations. Strong transmission ratio distortion and inter-chromosomal linkage disequilibrium in both F2s and RILs identified a novel two-locus genic incompatibility causing sex-independent gametophytic (haploid) lethality. The latter interaction eliminated three of the expected nine F2 genotypic classes via F1 gamete loss without detectable effects on the pollen number or viability of F2 double heterozygotes. Along with the mapping of numerous milder incompatibilities, these key findings illuminate the complex genetics of plant hybrid breakdown and are an important step toward understanding the genomic consequences of natural hybridization in this model system.

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.

Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples

The apple is an economically important fruit, and fruit russeting is not conducive to its appearance. Although studies have examined fruit russeting, its mechanism remains unclear. Two apple strains of the F1 hybrid population derived from 'Fuji' and 'Golden Delicious' were used in this study. We found that the skin of russet apples was rough and fissured, while that of non-russet apples was smooth and waxy. Chemical staining, LC- and GC-MS showed that both lignin and suberin were increased in russet apple skin. Meanwhile, genes involved in lignin and suberin synthetic pathways were upregulated in russet apple skin. Additionally, we found many differentially expressed genes (DEGs1) involved in hormone biosynthesis and signaling and stress responses in the two apple strains. We found that WRKY13 may influence russeting by regulating lignin synthesis. Our study identified several candidate metabolites and genes, which will provide a good foundation for further research.

Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus.

Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locusmapping revealed that stomata-associated geneloci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F1 hybrid populations of P. tomentosa showed that the DUF538, TRA2and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.

InDelGT: An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next-generation sequencing data.

Although several software packages are available for genotyping insertion/deletion (indel) polymorphisms in genomes using next-generation sequencing data, simultaneously calling indel genotypes across many individuals for use in genetic mapping remains challenging. We present an integrated pipeline, InDelGT, for the extraction of indel genotypes from a segregating population such as backcross or F2 lines, or from an F1 cross between outbred species. The InDelGT algorithm is implemented in three steps: generating an indel catalog, calling indel genotypes, and analyzing indel segregation. We demonstrated the use of the pipeline with an example data set from an F1 hybrid population of Populus and successfully constructed the two parental genetic linkage maps. InDelGT is a practical tool that can quickly genotype a large number of indel markers within a population following Mendelian segregation. The InDelGT pipeline is freely available on GitHub (https://github.com/tongchf/InDelGT).

Construction of a highly saturated genetic map and identification of quantitative trait loci for leaf traits in jujube.

Chinese jujube (Ziziphus jujuba Mill.), a member of the genus Ziziphus, which comes under the family Rhamnaceae, is the most important species in terms of its economic, ecological, and social benefits. To dissect the loci associated with important phenotypical traits and analyze their genetic and genomic information in jujube, a whole-genome resequencing (WGR) based highly saturated genetic map was constructed using an F1 hybrid population of 140 progeny individuals derived from the cross of ‘JMS2’ × ‘Jiaocheng 5’. The average sequencing depth of the parents was 14.09× and that of the progeny was 2.62×, and the average comparison efficiency between the sample and the reference genome was 97.09%. Three sets of genetic maps were constructed for a female parent, a male parent, and integrated. A total of 8,684 markers, including 8,158 SNP and 526 InDel markers, were evenly distributed across all 12 linkage groups (LGs) in the integrated map, spanning 1,713.22 cM with an average marker interval of 0.2 cM. In terms of marker number and density, this is the most saturated genetic map of jujube to date, nearly doubling that of the best ones previously reported. Based on this genetic map and phenotype data from 2019 to 2021, 31 leaf trait QTLs were identified in the linkage groups (LG1, 15; LG3, 1; LG5, 8; LG7, 4; LG8, 1, and LG11, 2), including 17 major QTLs. There were 4, 8, 14, and 5 QTLs that contributed to leaf length, leaf width, leaf shape index, and leaf area, respectively. Six QTLs clusters were detected on LG1 (8.05 cM–9.52 cM; 13.12 cM–13.99 cM; 123.84 cM–126.09 cM), LG5 (50.58 cM–50.86 cM; 80.10 cM–81.76 cM) and LG11 (35.98 cM–48.62 cM). Eight candidate genes were identified within the QTLs cluster regions. Annotation information showed that 4 genes (LOC107418196, LOC107418241, LOC107417968, and LOC112492570) in these QTLs are related to cell division and cell wall integrity. This research will provide a valuable tool for further QTL analysis, candidate gene identification, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in jujube.

A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii.

The genetic linkage maps of the traditional F2 population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F2 population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F1 hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map.

Combining Ability Analysis and Marker-Based Prediction of Heterosis in Yield Reveal Prominent Heterotic Combinations from Diallel Population of Rice

Combining ability along with heterosis was elucidated in the 21 F1 hybrid population of rice derived from a 7 × 7 diallel mating design. Furthermore, to formulate a strategy for marker-based prediction of heterosis, the molecular genetic diversity (GD) was then surveyed among the seven parental lines with RAPD markers. Analysis of combining ability revealed significant GCA and SCA variances and the ratio between the aforesaid genetic parameter was more than unity for most of the traits signifying the preponderance of additive gene action. Hybrid combination Double Rice × Pokkali was the best specific combiner for the traits pollen fertility percentage (%), panicle length (cm), filled grains/panicle (no.) and grain yield/hill (g) while Muktagacha × BRRI dhan29 and Basmati × Double Rice were the best specific combiners for grain length (mm) and 1000-grain weight (g), respectively. Regarding the magnitude of heterosis, Double Rice × Pokkali exhibited maximum heterobeltiosis for panicle length (33.33%) and the number of filled grains/panicle (144.01%). Furthermore, Pokkali × Chinigura was verified for producing the highest heterobeltiosis for tillers/hill (173.17%), as well as grain yield/hill (71.05%). The heatmap relying on molecular genetic diversity exposed the highest genetic distance between Chinigura and Pokkali followed by Muktagacha and Pokkali. Unweighted neighbor-joining trees clustered the parental lines into three groups indicating the presence of considerable genetic diversity among those seven parental genotypes. A positive and significant correlation was explored between molecular GD with specific combining ability as well as heterosis for all of the traits revealing the huge potentiality of hybrid performance prediction using RAPD markers with the present set of individuals. Thus, exploration of definite genomic regions underlying the candidate genes for respective traits relying on such RAPD-generated data following an advanced molecular marker approach would pave the path of mining out yielder heterotic combinations.

Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae).

Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.