Development of anthracnose disease resistance and heat tolerance chili through conventional breeding and molecular approaches: a review

Chili (Capsicum annuum L.) is the popular spicy vegetable crops belonging to family Solanaceae. Chili peppers are known for their pungency characteristic due to the presence of capsaicinoids that classifies them into hot or sweet pepper. Chili is used as spices, folk remedies for diseases, vegetables, and coloring agent showing a diverse role in human’s life. However, its production is hampered by different biotic stress and abiotic factors. Similarly, the unavailability of high yielding varieties, high temperature, and disease incidence, particularly, anthracnose disease, are the major constraints responsible for the low production of chili pepper. The advents of molecular markers, advancement in quantitative trait loci by classical genetic analysis, and conventional breeding have shown the number of genes for many important and major traits. While the newly developed genotyping technologies and next generation sequencing have led to the discovery of molecular basis for economic important characters in the chili genome and generate large scale data for genomic resources. Based on this background, this review summarizes progress in the development of anthracnose disease-resistant and heat-tolerant chili genotypes through conventional breeding and molecular approaches. This review would help plant breeders in understanding the phenotypic and genetic make-up of capsicum genotypes and provides opportunities for pyramiding two respected genes with the help of diversified phenotypic and molecular marker evaluation

Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders

Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., “Critical-Exon Genes (CEGs)”] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients’ pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients

Genetic analysis of anthracnose resistant and heat tolerant chili inbreed lines based on morpho-physiological characteristics

A better understanding of the various desirable characteristics present in chili (Capsicum annuum L.) genotypes has aided in developing more effective selection methods for crop improvement. Identifying genetically superior parents is critical in selecting the best parents and inbred lines for breeding purposes. This study was conducted over two planting seasons in glasshouse using morpho-physiological parameters to evaluate the heritability variation of selected chili genotypes based on their genetic diversity for future breeding program. Significant variances were observed in all the studied parameters across the chili pepper accessions with an inclusive range of diversity. The highest genotypic coefficient of variation (≥ 20%) was observed for all physiological and yield characteristics. While the highest phenotypic coefficient of variation (≥ 20%) was seen for all examined characteristics. All studied parameter had high broad sense heritability (˃ 55%) except total number of branches per plant (47.9%) while the moderate to high genetic advance were observer for all studied traits demonstrating that the extents of heritability and variability are due to their genetic makeup and environment had little influence on these characters. The evaluated genotypes were grouped into seven clusters based on the cluster analysis and Group I recorded highest yield with eight genotypes while Groups III, IV, V, VI, and VII recorded one each. Plant height and total branch number showed a highly significant positive correlation with the number of fruits per plant and yield per plant. Similarly, the number of fruits per plant had a highly significant positive correlation with fruit yield per plant. The study revealed that genetic variability might be usefully exploited through selection for further breeding purposes to increase yield and production

Estimation of heterosis and combining ability for improving yield, sweetness, carotenoid and antioxidant qualities in pumpkin hybrids (Cucurbita moschata Duch. Ex Poir.)

A full diallel mating design was used to hybridize seven pumpkin inbred parental lines, yielding 42 F1 hybrids, including reciprocals. The generated F1 hybrids, parental lines and commercial check hybrid were evaluated in two environments to investigate the per se performances, combining ability effects and magnitude of heterosis over mid-parent, better-parent and commercial check hybrids for yield, yield attributed, sweetness, total carotenoid and antioxidant traits, using a randomized complete block design with three replications. The analysis of variance for most of the examined traits revealed highly significant differences (p ≤ 0.01) for GCA, SCA, reciprocal, maternal and non-maternal variances and their interaction with the environment. Since the inheritance of yield and its contributing fruit quality, and antioxidant traits is governed by non-additive gene action, it suggests heterosis breeding would be useful in obtaining further improvements in pumpkin. From the experiment, it was found that the paternal lines P1 (Gold Butter 315) for dry matter content and DPPH (%), P4 (Asian pumpkin) for total carotenoid content, P6 (Sarawak) for fruit number per plant and P7 (Australia-1) for single fruit weight, fruit flesh thickness, yield per plant and total soluble solid were shown to be good general combiners. In respect to per se performance, combining ability effects and magnitude of heterosis over mid-parent, better-parent and commercial check, the cross P2 (928 Fuxiang) × P1 (Gold Butter 315) and P4 (Asian pumpkin) × P5 (Sarawak) for single fruit weight and yield per plant, the cross P5 (Sarawak) × P2 (928 Fuxiang) for fruits number per plant, P1 (Gold Butter 315) × P7 (Australia-1) and P1 (Gold Butter 315) × P6 (Sarawak) for total soluble solid and dry matter content, P7 (Australia-1) × P2 (928 Fuxiang) for total carotenoid content and P3 (Ser Bajadi) × P1 (Gold Butter 315) for DPPH (antioxidant) were identified to be highly significant positive specific combiners and the highest performers, and these crosses may be exploited as commercial hybrids

Genetic diversity analysis among Capsicum annuum mutants based on morpho-physiological and yield traits

It is crucial to assess genetically superior parents when developing novel hybrids. This experiment was conducted to find out the diversity of 27 Capsicum annuum mutant lines derived from two varieties.To achieve the objective, 23 morpho-physiological and yield traits were recorded through two planting seasons. Highly significant differences (p < 0.01) were recorded among the studied traits. There was a strong to moderately positive phenotypic association between yield and all other morphological traits except first bifurcation length, stem diameter, pedicle length, flowering date, and maturity date. A higher Genotypic Coefficient of Variation (GCV) and Phenotypic Coefficient of Variation (PCV), combined with moderate to high heritability and high hereditary progress, have been found in the number of fruits per plant, fruit yield per plant, and number of seeds per fruit. High heritability was found in yield characteristics, vis-à-visnumber of seeds per fruit, number of fruits per plant, and indicated high genetic advance. The studied genotypes were divided into six groups after the cluster analysis. Based on the correlation matrix of 23 quantitative characteristics, principal component analysis revealed that the percentage of variation for PC1 and PC2 is 28%and 19%, respectively, andPC1 represents the largest percentage of the overall total variation. The calculated genetic distance also explains the potential of heterosis breeding. The revealed findings might be helpful for breeders to target quantitative characters and the parental lines of C. annuum during the execution of their future breeding programmes for developing high-yielding and climate-resilient chilli varieties

Growth and yield performances, pathogenicity, heat tolerance, antioxidant activity, and pungency level of anthracnose resistant and heat tolerant inbreed lines and their F1 hybrids of chili (Capsicum annuum L.)

Chili pepper (Capsicum annuum L.) cultivation is hampered by biotic and abiotic stressors, with poor performance caused by high temperatures exceeding 42 °C and anthracnose infestation. Chemical constituents such as antioxidants, phenols, capsaicin, and dihydrocapsaicin have a relationship with biotic and abiotic tolerance or resistance. Experiment was conducted with anthracnose resistant (CP-36, DP-37, DP-57, AP-25 and BP-23), heat tolerant inbreed lines (Putra chili 1, Putra chili 4, Putra chili 7, Putra chili 9 and Putra chili 10) and their hybrids to find anthracnose-resistant, heat-tolerant chili genotypes with high yield and pungency levels. For this purposes, pathogens were injected into both unripe and ripe chili fruits to determine their pathogenicity. On the other hand, four-week-old seedling was raised for a heat tolerance test to determine the percentage of partial damage (%) and thermo-stability index of the cell membrane (%). The research also included morphological, yield and yield contributing, physiological, and biochemical assessment in order to identify superior chili hybrids. All growth, yield, and physiological traits showed excellent genetic progress and heritability, but correlation analysis showed a highly significant positive link between yield per plant, plant height, the total number of branches, and the number of fruits per plant. Lesion area of unripe fruits were varied from 0.00 (cm2) to 0.24 (cm2) and 0.00 (cm2) to 0.18 (cm2) for the pathogen, UPMC1191 (Colletotrichum fructicola) and UPMC1192 (Colletotrichum sojae), respectively and also indicated that differential resistant to anthracnose pathogen. In a heat tolerance test, all of the hybrids with the improved heat tolerant line performed better in terms of cell membrane thermo-stability, partial damage at various temperature gradients, and canopy temperature depression. In terms of biochemical state, DP-37 × Putra chili 7; AP-25 × Putra chili 10 had a moderate level of pungency, while some other parents and hybrids had mild level of pungency. After screening with Colletotrichum pathogen, heat tolerance test, biochemical constitute and yield performance, following hybrids would be better for commercial production to meet up the demand such as CP-36 × Putra chili 1; CP-36 × Putra chili 7; CP-36 × Putra chili 9; DP-37 × Putra chili 1; DP-37 × Putra chili 10; DP-37 × Putra chili 4; DP-37 × Putra chili 7; DP-37× Putra chili 9; DP-57 × Putra chili 7; DP-57 × Putra chili 9; DP-57 × Putra chili 10; AP-25 × Putra chili 9; AP-25 × Putra chili 4; BP-23 × Putra chili 7; BP-23 × Putra chili 9; BP-23 × Putra chili 1 and would be use in future chili breeding program

Genetic Diversity Analysis among Capsicum annuum Mutants Based on Morpho-Physiological and Yield Traits

It is crucial to assess genetically superior parents when developing novel hybrids. This experiment was conducted to find out the diversity of 27 Capsicum annuum mutant lines derived from two varieties.To achieve the objective, 23 morpho-physiological and yield traits were recorded through two planting seasons. Highly significant differences (p &lt; 0.01) were recorded among the studied traits. There was a strong to moderately positive phenotypic association between yield and all other morphological traits except first bifurcation length, stem diameter, pedicle length, flowering date, and maturity date. A higher Genotypic Coefficient of Variation (GCV) and Phenotypic Coefficient of Variation (PCV), combined with moderate to high heritability and high hereditary progress, have been found in the number of fruits per plant, fruit yield per plant, and number of seeds per fruit. High heritability was found in yield characteristics, vis-&agrave;-visnumber of seeds per fruit, number of fruits per plant, and indicated high genetic advance. The studied genotypes were divided into six groups after the cluster analysis. Based on the correlation matrix of 23 quantitative characteristics, principal component analysis revealed that the percentage of variation for PC1 and PC2 is 28%and 19%, respectively, andPC1 represents the largest percentage of the overall total variation. The calculated genetic distance also explains the potential of heterosis breeding. The revealed findings might be helpful for breeders to target quantitative characters and the parental lines of C. annuum during the execution of their future breeding programmes for developing high-yielding and climate-resilient chilli varieties