Generations Of Selfing Research Articles

Improving Pepper Inbreds for Resistance to Pepper Yellow Leaf Curl Thailand Virus (PepYLCTHV) through Challenged Inoculations

Chili peppers (Capsicum annuum L.) are an economically important crop worldwide. Pepper yellow leaf curl Thailand virus (PepYLCTHV), a Begomovirus causing yellow leaf mosaic disease of chili pepper, has been reported to incur 95% economic loss under epiphytotic conditions. Thirty-one chili genotypes were screened for resistance to PepYLCTHV disease through inoculation using 10–15 viruliferous whiteflies per plant. We purified two resistant lines (PEP6 and PEP12) through four generations of selfing and selection. At 28 days after inoculations, two chili genotypes (PEP6 and PEP12) had low disease severity and percentage of disease incidence (DI) compared to four susceptible checks, viz., Yodsonkeam80, Homsupan, Huareau12, and Pong Charian, which had a disease severity score of 5 with 100% DI. Thirty initial plants of PEP6 showed an average disease severity of 3.64 with 69.33% DI, and PEP12 showed an average disease severity of 3.83 with 77.67% DI. From these populations, we selected nine highly resistant plant of PEP6 and seven plants of PEP12 having a disease severity of 0 through pure-line selection for four selfing generations. The ratio of resistance (R) to susceptibility (S) consequently decreased. In PEP6, the ratio decreased from 1R:2S to 1R:1S, while in PEP12 the ratio decreased from 1R:3S to 1R:1S. These lines have potential for release as resistant lines for improving chili pepper resistance to PepYLCTHV and for developing makers associated with the resistant trait.

Regional active transcription associates with homoeologous exchange breakpoints in synthetic Brassica tetraploids.

Polyploidization plays a crucial role in plant evolution and is becoming increasingly important in breeding. Structural variations and epigenomic repatterning have been observed in synthetic polyploidizations. However, the mechanisms underlying the occurrence and their effects on gene expression and phenotype remain unknown. Here, we investigated genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics in leaf organs of progeny from the first eight generations of synthetic tetraploids derived from Chinese cabbage (Brassica rapa L. ssp. pekinensis) and cabbage (Brassica oleracea L. var. capitata). One- or two-copy DelDups, with a mean size of 5.70 Mb (400 kb to 65.85 Mb), occurred from the first generation of selfing and thereafter. The duplication of a fragment in one subgenome consistently coincided with the deletion of its syntenic fragment in the other subgenome, and vice versa, indicating that these DelDups were generated by homoeologous exchanges (HEs). Interestingly, the larger the genomic syntenic region, the higher the frequency of DelDups, further suggesting that the pairing of large homoeologous fragments is crucial for HEs. Moreover, we found that the active transcription of continuously distributed genes in local regions is positively associated with the occurrence of HE breakpoints. In addition, the expression of genes within DelDups exhibited a dosage effect, and plants with extra parental genomic fragments generally displayed phenotypes biased toward the corresponding parent. Genome-wide methylation fluctuated remarkably, which did not clearly affect gene expression on a large scale. Our findings provide insights into the early evolution of polyploid genomes, offering valuable knowledge for polyploidization-based breeding.

Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbred Caenorhabditis elegans mutation accumulation lines.

The distribution of fitness effects of new mutations plays a central role in evolutionary biology. Estimates of the distribution of fitness effect from experimental mutation accumulation lines are compromised by the complete linkage disequilibrium between mutations in different lines. To reduce the linkage disequilibrium, we constructed 2 sets of recombinant inbred lines from a cross of 2 Caenorhabditis elegans mutation accumulation lines. One set of lines ("RIAILs") was intercrossed for 10 generations prior to 10 generations of selfing; the second set of lines ("RILs") omitted the intercrossing. Residual linkage disequilibrium in the RIAILs is much less than in the RILs, which affects the inferred distribution of fitness effect when the sets of lines are analyzed separately. The best-fit model estimated from all lines (RIAILs + RILs) infers a large fraction of mutations with positive effects (∼40%); models that constrain mutations to have negative effects fit much worse. The conclusion is the same using only the RILs. For the RIAILs, however, models that constrain mutations to have negative effects fit nearly as well as models that allow positive effects. When mutations in high linkage disequilibrium are pooled into haplotypes, the inferred distribution of fitness effect becomes increasingly negative-skewed and leptokurtic. We conclude that the conventional wisdom-most mutations have effects near 0, a handful of mutations have effects that are substantially negative, and mutations with positive effects are very rare-is likely correct, and that unless it can be shown otherwise, estimates of the distribution of fitness effect that infer a substantial fraction of mutations with positive effects are likely confounded by linkage disequilibrium.

Heritable Phenotypic Variations in the Self-Pollinated Progeny from Grafted Cucumber with Pumpkin as Rootstock

This study investigated whether grafting cucumber (Cucumis sativus L.) onto pumpkin (Cucurbita moschata Duch.) rootstocks can induce phenotypic variations in the self-bred cucumber progeny. The phenotypic traits of the self-pollinated progeny of grafted ‘Zhenghuang 1409’ cucumber were significantly different from those of the naturally rooted ‘Zhenghuang 1409’ parent line. Compared with the ‘Zhenghuang 1409’ cucumber inbred line, the first self-pollinated and naturally rooted generation of grafted cucumber displayed reduced length and width of the leaf at the node of the second female flower, a tapered petiole and stem, increased internode length, shorter plants, decreased fruit diameter, longer fruit stalk, thicker pulp, decreased seed length and width, and a lower 100-grain weight. Similar changes in most of these phenotypic traits were observed in the second generation of self-pollinated plants from grafted cucumber. By observing plant phenotypic traits, two leaf phenotypic variations were observed in the first generation of selfed grafted cucumber, and these two phenotypes were inherited in the second selfed generation.

Development of near homozygous lines for diploid hybrid TPS breeding in potatoes

Diploid inbred-based F1 hybrid True Potato Seed (DHTPS) breeding is a novel technique to transform potato breeding and cultivation across the globe. Significant efforts are being made to identify elite diploids, dihaploids and develop diploid inbred lines for heterosis exploitation in potatoes. Self-incompatibility is the first obstacle for developing inbred lines in diploid potatoes, which necessitates the introgression of a dominant S locus inhibitor gene (Sli) for switching self-incompatibility to self-compatibility. We evaluated a set of 357 diploid clones in different selfing generations for self-compatibility and degree of homozygosity using Kompetitive Allele Specific PCR (KASP) Single Nucleotide Polymorphism (SNP) markers. A subset of 10 KASP markers of the Sli candidate region on chromosome 12 showed an association with the phenotype for self-compatibility. The results revealed that the selected 10 KASP markers for the Sli gene genotype could be deployed for high throughput rapid screening of self-compatibility in diploid populations and to identify new sources of self-compatibility. The homozygosity assessed through 99 KASP markers distributed across all the chromosomes of the potato genome was 20–78 % in founder diploid clones, while different selfing generations, i.e., S0, S1, S2 and S3 observed 36.1–80.4, 56.9–82.8, 59.5–85.4 and 73.7–87.8 % average homozygosity, respectively. The diploid plants with ∼80 % homozygosity were also observed in the first selfing generation, which inferred that homozygosity assessment in the early generations itself could identify the best plants with high homozygosity to speed up the generation of diploid inbred lines.

Genome-Wide Association Studies on the Kernel Row Number in a Multi-Parent Maize Population.

Kernel row number (KRN) is a crucial trait in maize that directly influences yield; hence, understanding the mechanisms underlying KRN is vital for the development of high-yielding inbred lines and hybrids. We crossed four excellent panicle inbred lines (CML312, CML444, YML46, and YML32) with Ye107, and after eight generations of selfing, a multi-parent population was developed comprising four subpopulations, each consisting of 200 lines. KRN was accessed in five environments in Yunnan province over three years (2019, 2021, and 2022). The objectives of this study were to (1) identify quantitative trait loci and single nucleotide polymorphisms associated with KRN through linkage and genome-wide association analyses using high-quality genotypic data, (2) identify candidate genes regulating KRN by identifying co-localized QTLs and SNPs, and (3) explore the pathways involved in KRN formation and identify key candidate genes through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Our study successfully identified 277 significant Quantitative trait locus (QTLs) and 53 significant Single Nucleotide Polymorphism (SNPs) related to KRN. Based on gene expression, GO, and KEGG analyses, SNP-177304649, SNP-150393177, SNP-135283055, SNP-138554600, and SNP-120370778, which were highly likely to be associated with KRN, were identified. Seven novel candidate genes at this locus (Zm00001d022420, Zm00001d022421, Zm00001d016202, Zm00001d050984, Zm00001d050985, Zm00001d016000, and Zm00014a012929) are associated with KRN. Among these, Zm00014a012929 was identified using the reference genome Mo17. The remaining six genes were identified using the reference genome B73. To our knowledge, this is the first report on the association of these genes with KRN in maize. These findings provide a theoretical foundation and valuable insights into the genetic mechanisms underlying maize KRN and the development of high-yielding hybrids through heterosis.

Prediction of matrilineal specific patatin-like protein governing in-vivo maternal haploid induction in maize using support vector machine and di-peptide composition

The mutant matrilineal (mtl) gene encoding patatin-like phospholipase activity is involved in in-vivo maternal haploid induction in maize. Doubling of chromosomes in haploids by colchicine treatment leads to complete fixation of inbreds in just one generation compared to 6–7 generations of selfing. Thus, knowledge of patatin-like proteins in other crops assumes great significance for in-vivo haploid induction. So far, no online tool is available that can classify unknown proteins into patatin-like proteins. Here, we aimed to optimize a machine learning-based algorithm to predict the patatin-like phospholipase activity of unknown proteins. Four different kernels [radial basis function (RBF), sigmoid, polynomial, and linear] were used for building support vector machine (SVM) classifiers using six different sequence-based compositional features (AAC, DPC, GDPC, CTDC, CTDT, and GAAC). A total of 1170 protein sequences including both patatin-like (585 sequences) from various monocots, dicots, and microbes; and non-patatin-like proteins (585 sequences) from different subspecies of Zea mays were analyzed. RBF and polynomial kernels were quite promising in the prediction of patatin-like proteins. Among six sequence-based compositional features, di-peptide composition attained > 90% prediction accuracies using RBF and polynomial kernels. Using mutual information, most explaining dipeptides that contributed the highest to the prediction process were identified. The knowledge generated in this study can be utilized in other crops prior to the initiation of any experiment. The developed SVM model opened a new paradigm for scientists working in in-vivo haploid induction in commercial crops. This is the first report of machine learning of the identification of proteins with patatin-like activity.

Development of Genotypes for Foliar Disease Resistance in Mungbean [Vigna radiata (L.) Wilczek] through Recombination and Mutation Breeding

Background: Despite the best efforts for improving the greengram varieties, the yield potential of this crop remains low owing to both biotic and abiotic factors. Yield losses caused due to various diseases were estimated to be 24-67 per cent in anthracnose, 80-100 per cent in mungbean yellow mosaic virus and 40 per cent due to powdery mildew So, the use of resistant cultivars is the most effective and eco-friendly method of managing the disease. Methods: A series of field experiments spanned over seven years (2014-2021) were conducted at Main Agricultural Research Station, University of Agricultural Sciences, Dharwad, Karnataka. In the first set of experiments, the material comprised of eight varieties of greengram which were treated with 20kR gamma radiation. M1was planted in Kharif 2014 and each variety was bulk harvested. M2 was planted in summer 2014 and individual plant selection was carried out. Mutant families were advanced to the further generation in Kharif 2015 and Rabi 2015. The M2 mutants were scored for their reaction to anthracnose, cercospora leaf spot and powdery mildew diseases with respective susceptible and resistant checks. In another set of experiments aimed at developing MYMV tolerant genotypes, an investigation was carried out with 168 F2 individuals derived from crossing Vigna trilobata and DGGV2. One row infector line of DGGV-2 was raised after every three test entries to study the reaction to MYMV. Three rows of susceptible check was planted all around the border to ensure enough inoculum load. Of the 168 F2 individuals, two lines showed resistance to MYMV. They were stabilized through a series of selfing generations. Result: Evaluation of advanced breeding lines for their reaction to various foliar diseases revealed that the advanced breeding lines DGG-203, DGG-206, DGG-208, DGG-21, DGG-80, DGG-273, DGG-274, DGG-275, DGG-262, DGG-263, DGG-264, DGG-82, DGG-200, TARM-1 (C), DGG-215-5, DGG-302, DGG-152, IPM-3-2, DGG-20, DGG-73, IPM-14-10, DGG-121, DGG-250, DGG-109, DGG-96 had seed yields ranging from 9.8 g to 12.4 g and moderately resistant to both anthracnose and CLS. The breeding lines DGG-203, DGG-206, DGG-21, DGG-273, IPM-3-2 (Check), DGG-96 have recorded combined resistance to anthracnose, cercospora leaf spot and powdery mildew diseases.

Metabolic priming in G6PDH isoenzyme-replaced tobacco lines improves stress tolerance and seed yields via altering assimilate partitioning.

We investigated the basis for better performance of transgenic Nicotiana tabacum plants with G6PDH-isoenzyme replacement in the cytosol (Xanthi::cP2::cytRNAi, Scharte etal., 2009). After six generations of selfing, infiltration of Phytophthora nicotianae zoospores into source leaves confirmed that defence responses (ROS, callose) are accelerated, showing as fast cell death of the infected tissue. Yet, stress-related hormone profiles resembled susceptible Xanthi and not resistant cultivar SNN, hinting at mainly metabolic adjustments in the transgenic lines. Leaves of non-stressed plants contained twofold elevated fructose-2,6-bisphosphate (F2,6P2 ) levels, leading to partial sugar retention (soluble sugars, starch) and elevated hexose-to-sucrose ratios, but also more lipids. Above-ground biomass lay in between susceptible Xanthi and resistant SNN, with photo-assimilates preferentially allocated to inflorescences. Seeds were heavier with higher lipid-to-carbohydrate ratios, resulting in increased harvest yields - also under water limitation. Abiotic stress tolerance (salt, drought) was improved during germination, and in floated leaf disks of non-stressed plants. In leaves of salt-watered plants, proline accumulated to higher levels during illumination, concomitant with efficient NADP(H) use and recycling. Non-stressed plants showed enhanced PSII-induction kinetics (upon dark-light transition) with little differences at the stationary phase. Leaf exudates contained 10% less sucrose, similar amino acids, but more fatty acids - especially in the light. Export of specific fatty acids via the phloem may contribute to both, earlier flowering and higher seed yields of the Xanthi-cP2 lines. Apparently, metabolic priming by F2,6P2 -combined with sustained NADP(H) turnover-bypasses the genetically fixed growth-defence trade-off, rendering tobacco plants more stress-resilient and productive.

Phenotype Evaluation and Estimation of Genetic Parameter of Baby Corn From Two Generation Selfing and Sibbing

Baby corn is consumed widely in Indonesia, but special corn varieties for baby corn production are not available until now. The objectives of this study were to evaluate phenotypes, estimate the genetic parameters from two generations of selfing and sibbing, and identify the genotypes to develop as baby corn variety. This study was conducted using a completely randomized block design with three replications. Genetic materials used consist of 19 genotypes. They were four genotypes S0, HS1, S1, S2 and three genotypes of HS2. Progenitors(S0) were Laksmi, Golden, Hawaii, and Baruna belonging sweet corn type. Baby corn’s phenotypes from two generations sibbing were more vigor than selfing. Families of HS2 dan S2 have a higher percentage of class A marketable cobs than generations before. Two generations sibbing and selfing increased genetic variances and broad-sense heritability. Families of HS2 had better phenotypic performance than S2, the percentage of class A marketable cobs was higher than S0 and HS1, number of cobs per plant was the highest broad-sense heritability estimation. HS2 families were considered to develop as open-pollinated baby corn varieties.

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding.

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

Establishment and inheritance of minichromosomes from Arabidopsis haploid induction

Minichromosomes are small, sometimes circular, rearranged chromosomes consisting of one centromere and short chromosomal arms formed by treatments that break DNA, including plant transformation. Minichromosomes have the potential to serve as vectors to quickly move valuable genes across a wide range of germplasm, including into adapted crop varieties. To realize this potential, minichromosomes must be reliably generated, easily manipulated, and stably inherited. Here we show a reliable method for minichromosome formation in haploids resulting from CENH3-mediated genome elimination, a process that generates genome instability and karyotypic novelty specifically on one parental genome. First, we identified 2 out of 260 haploids, each containing a single-copy minichromosome originating from centromeric regions of chromosomes 1 and 3, respectively. The chromosome 1 minichromosome we characterized did not pair at meiosis but displayed consistent transmission over nine selfing generations. Next, we demonstrated that CENH3-based haploid induction can produce minichromosomes in a targeted manner. Haploid inducers carrying a selectable pericentromeric marker were used to isolate additional chromosome-specific minichromosomes, which occurred in 3 out of 163 haploids. Our findings document the formation of heritable, rearranged chromosomes, and we provide a method for convenient minichromosome production.

Genetic architecture of terpene chemistry and growth traits and the impact of inbreeding on these traits in western redcedar (Thuja plicata).

Western redcedar (WRC; Thuja plicata) is a conifer of the Pacific Northwest of North America prized for its durable and rot-resistant wood. WRC has naturally low outcrossing rates and readily self-fertilizes in nature. Challenges faced in WRC breeding and propagation involve selecting trees for accelerated growth while also ensuring enhanced heartwood rot resistance and resistance to ungulate browsing, as well as mitigating potential effects of inbreeding depression. Terpenes, a large and diverse class of specialized metabolites, confer both rot and browse resistance in the wood and foliage of WRC, respectively. Using a Bayesian modelling approach, we isolated single nucleotide polymorphism (SNP) markers estimated to be associated with three different foliar terpene traits and four different heartwood terpene traits, as well as two growth traits. We found that all traits were complex, being associated with between 1700 and 3600 SNPs linked with putatively causal loci, with significant polygenic components. Growth traits tended to have a larger polygenic component while terpene traits had larger major gene components; SNPs with small or polygenic effect were spread across the genome, while larger-effect SNPs tended to be localized to specific linkage groups. To determine whether there was inbreeding depression for terpene chemistry or growth traits, we used mixed linear models for a genomic selection training population to estimate the effect of the inbreeding coefficient F on foliar terpenes, heartwood terpenes and several growth and dendrochronological traits. We did not find significant inbreeding depression for any assessed trait. We further assessed inbreeding depression across four generations of complete selfing and found that not only was inbreeding depression not significant but that selection for height growth was the only significant predictor for growth during selfing, suggesting that inbreeding depression due to selfing during operational breeding can be mitigated by increased selection intensity.

Evaluation of the fifth selfing generation of Madura Local Maize, Indonesia

The assembly of hybrid maize varieties with high production and early maturity is the right step to increase maize production on Madura Island, Indonesia. Assessment of the fifth generation selfing maize genotype aims to obtain potential parents that can be used in assembling hybrid maize varieties. This study aimed to evaluate the fifth selfing generation of Madura local maize, Indonesia. The study used a randomized complete block design with ten genotypes as treatment and repeated three times, so there were ten experimental units. The ten genotypes were G1= Tb-1-10-5, G2 = Tb-2-21-5, G3 = EL-1-26-5, G4 = EL-3-2-5, G5 = DL-2-11-5, G6 = DK-1-5-5, G7 = CTK-1-4-5, G8 = DBR-1-12-5, G9 = KRA-1-2-5, dan G10 = GL-1-6-5. Characters observed in this study were plant height, days of 50% tasseling, days of silking, harvest age, ear length, ear diameter, 100-kernel weight, and production per hectare. The eight characters observed in ten fifth-generation selfing maize had a low coefficient of variance (0.16-6.62%), indicating that the variation within the genotype was small. The genotypic coefficient of variation (GCV) is greater than the phenotypic coefficient of variation (PCV) in all observed characters. The heritability value in the broad sense of all observed characters is 0.81-0.99 (high). Production per hectare has a significant positive correlation with plant height, days to 50% tasseling, days to 50% silking, harvest age, ear length. G1, G2, and G5 were potential genotypes that could be used as parents in the assembly of high-production and early-maturity maize varieties.

Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: An example in cacao (Theobroma cacao L.).

Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3–5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC´s germplasm collection and 49 inbred offspring of six S1 or S2 cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727± 0.182) and 19 of them with homozygosity ≥90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S1 and S2 families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81–93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees.

Genomic prediction for the Germplasm Enhancement of Maize project.

The Germplasm Enhancement of Maize (GEM) project was initiated in 1993 as a cooperative effort of public- and private-sector maize (Zea mays L.) breeders to enhance the genetic diversity of the U.S. maize crop. The GEM project selects progeny lines with high topcross yield potential from crosses between elite temperate lines and exotic parents. The GEM project has released hundreds of useful breeding lines based on phenotypic selection within selfing generations and multienvironment yield evaluations of GEM line topcrosses to elite adapted testers. Developing genomic selection (GS) models for the GEM project may contribute to increases in the rate of genetic gain. Here we evaluated the prediction ability of GS models trained on 6 yr of topcross evaluations from the two GEM programs in Raleigh, NC, and Ames, IA, documenting prediction abilities ranging from 0.36 to 0.75 for grain yield and from 0.78 to 0.96 for grain moisture when models were cross-validated within program and heterotic group. Predicted genetic gain from GS ranged from 0.95 to 2.58 times the gain from phenotypic selection. Prediction ability across program and heterotic group was generally poorer than within groups. Based on observed genomic relationships between GEM breeding lines and their tropical ancestors, GS for either yield or moisture would reduce recovery of exotic germplasm only slightly. Using GS models trained within program, the GEM programs should be able to more effectively deliver on its mission to broaden the genetic base of U.S. germplasm.

Inheritance of traits related to yield and fatty acid profile of winter squash seed oil

The objective of this study was to determine the inheritance of traits related to seed oil yield and fatty acid profile components and to estimate the genetic relationships between these traits in Cucurbita moschata D. This study assessed six generations derived from crosses between parents with contrasting traits under study. F1 plants were obtained from the crossing between BGH 7319 (P1) and ‘Tronco Verde’ (P2), which were subsequently self-fertilized to obtain the F2 generation. F1 plants were also backcrossed with the P1 and P2 parents to obtain the BC1 and BC2 generations, respectively. In general, additive effects were predominant for most of the traits, and thus, the development of inbred lines is the recommended strategy for genetic improvement of these traits. Dominance effects were significant even under low expression. This demonstrates that the performance of progeny tests throughout the selfing generations will enable the distinction between genotypes, thus providing greater efficiency in selection and, consequently, greater genetic gains. In addition, overdominance was observed in oil content; therefore, the development of hybrids with genotypes causing high oil content is attainable. In general, the estimates of genetic correlations had a high magnitude and were favorable to the increase in functional oil productivity, associated with better quality of fatty acid profiles. Recurrent intrapopulation selection aimed at the development of open-pollinated varieties with high productivity, associated with greater stability of the functional oil in C. moschata, may be useful.

The western redcedar genome reveals low genetic diversity in a self-compatible conifer.

We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity.

Study of genetic architecture of grain yield and quality traits through generation mean analysis in rice (Oryza sativa L.)

A perusal of gene effects in generation mean analysis for three crosses viz., BPT 5204 x IR 36, BPT 5204 x NLR 34449 and RNR 2465 x IR 64 revealed the presence of a significant proportion of epistatic effects besides the major components viz., additive (d) and dominance (h) gene effects for important yield and quality attributes. Partitioning of variance indicating that the mean values (m) for gene effects were highly significant in all the three crosses for most of the traits, the results of dominance (h) and dominance × dominance (l) type interactions revealed that duplicate type of epistasis was prevalent for most of the traits in all the six crosses except in RNR 2465 x IR 64 for the number of filled grains per panicle; BPT 5204 x NLR 34449 for kernel breadth and kernel elongation ratio and BPT 5204 x IR 36 for harvest index where, complementary gene action played a vital role in the inheritance of the traits. Therefore, improvement of these traits appears to overwhelmed with difficulties as simple selection techniques will not be able to fix superior lines in the early segregating generations. Postponement of selection for superior lines to later generations in pedigree breeding will be effective. However, one or two cycles of recurrent selection followed by pedigree breeding will be effective and useful to utilize both additive and non-additive gene effects. The predominance of dominance and epistatic interactions in all the crosses for quality traits indicates that selection would be more effective if the dominance and epistatic effects are first reduced by a few generations of selfing. &nbsp;Keywords: Rice, generation mean analysis, gene action

Pyramiding disease resistance in tomato by duplex PCR targeting resistance genes and exploiting gene linkage

Tomato is the second most important vegetable crop in the world after potato. Its production is hindered by fungal and viral diseases. Control of these diseases requires a significant investment that represents up to 40% of the production costs. Marker-assisted gene pyramiding is a powerful breeding tool which allow the rapid constitution of breeding lines with broad spectrum of resistance against diseases. Nevertheless, the accuracy and rapidity of introgression of genes of interest are some of the most critical barriers to successful application. In this paper, we use a simple and rapid method that combines duplex PCR for two important virus resistance genes (i.e., Sw-5 and Tm-22) and uses the linkage between genes Tm-22 and Forl to speed the introgression of these resistance genes into a “Pomodoro di Sorrento” tomato line. The method was used through six generations of backcrossing followed by three generations of selfing and resulted in a homozygous resistant line.