Selection Of Superior Genotypes Research Articles

Phenological growth stages of cardamom (Elettaria cardamomum Maton): Detailed identification and description using the extended BBCH scale

AbstractCardamom (Elettaria cardamomum Maton) is an important spice crop with high market value. In this study, we describe the phenological growth stages of cardamom using a three‐digit extended Biologische Bundesanstalt, Bundessortenamt und CHemische Industrie (BBCH) scale, which includes eight principal growth stages, comprising four vegetative, two reproductive and two capsule development stages. Additionally, we identified 45 secondary stages within these principal growth stages, providing a comprehensive characterisation of the crop's growth progression, including bud development, leaf emergence, tillering and shoot development, while the reproductive stages included inflorescence emergence and flowering. The capsule development stage details the maturation process of capsules. The study also highlights the parallel occurrence of tillering, shoot development and inflorescence emergence stages during specific growth phases. The knowledge of growth stages facilitates timely interventions, optimising crop management strategies and enhancing overall crop productivity. Additionally, these findings offer valuable insights for breeding programmes and the selection of superior genotypes, contributing to the sustainable cultivation and economic viability of cardamom as an important export‐oriented spice crop.Highlights BBCH scale provides uniform coding for different growth stages of cardamom. Identified and described eight principal growth stages (PGS). PGS comprises of 4 vegetative, 2 reproductive and 2 capsule development stages. 45 secondary stages were identified within 8 principal growth stages. Tillering, shoot development and inflorescence emergence occurs parallelly.

Genetic Variability Studies in Yellow Seeded Linseed

The experimental materials consisted of 40 yellow seeded genotypes of linseed taken from “AICRP on linseed, Department of Genetics and Plant Breeding, IGKV, Raipur”, Chhattisgarh, India along with one check variety Surabhi. Seed yield is an important trait and the cumulative result of a number of component traits controlled by polygenes and influenced greatly by the environmental factors. Hence, yield alone would not be effective for selection of superior genotypes. In order to make the selection effective one has to give emphasis on the yield attributing traits. According to analysis of variance, “significant differences exist for all the parameters investigated from yellow seeded linseed genotypes.” It demonstrates that the yellow seeded genotypes of linseed have sufficient variability in seed yield and contributing characteristics. 1000 Seed weight (7.7g) and seed yield (15g) were the highest in the YLS-31 and YLS-23 genotypes, respectively. The highest GCV was found in number of secondary branches per plant (39.5%) followed by seed yield (32.1%), harvest index (21.6%), and number of primary branches per plant (24.3%). The highest PCV was found in the number of primary branches per plant (47%). Number of secondary branches per plant (43.2%), 1000 seed weight (37.9%), number of capsules per plant (33.9%) and harvest index (22.8%) were the next most important factor.

Review of applications of artificial intelligence (AI) methods in crop research.

Sophisticated and modern crop improvement techniques can bridge the gap for feeding the ever-increasing population. Artificial intelligence (AI) refers to the simulation of human intelligence in machines, which refers to the application of computational algorithms, machine learning (ML) and deep learning (DL) techniques. This is aimed to generalise patterns and relationships from historical data, employing various mathematical optimisation techniques thus making prediction models for facilitating selection of superior genotypes. These techniques are less resource intensive and can solve the problem based on the analysis of large-scale phenotypic datasets. ML for genomic selection (GS) uses high-throughput genotyping technologies to gather genetic information on a large number of markers across the genome. The prediction of GS models is based on the mathematical relation between genotypic and phenotypic data from the training population. ML techniques have emerged as powerful tools for genome editing through analysing large-scale genomic data and facilitating the development of accurate prediction models. Precise phenotyping is a prerequisite to advance crop breeding for solving agricultural production-related issues. ML algorithms can solve this problem through generating predictive models, based on the analysis of large-scale phenotypic datasets. DL models also have the potential reliability of precise phenotyping. This review provides a comprehensive overview on various ML and DL models, their applications, potential to enhance the efficiency, specificity and safety towards advanced crop improvement protocols such as genomic selection, genome editing, along with phenotypic prediction to promote accelerated breeding.

Genetic parameters for host-response to acanthocephaliasis caused by the endoparasite Neoechinorhynchus buttnerae in the Amazon fish Colossoma macropomum

Tambaqui (Colossoma macropomum) is the main native fish produced by Amazon aquaculture. However, the production chain of this fish has been significantly affected by acanthocephaliasis, caused by the endoparasite Neoechinorhynchus buttnerae. The selection of superior genotypes for resistance and resilience to acanthocephaliasis is a fundamental approach to improve production in the context of environmental sustainability and food security. Thus, the objectives of this study were to 1) conduct an experimental challenge against the endoparasite N. buttnerae in tambaqui, and 2) determine the genetic parameters of disease traits caused by N. buttnerae in an experimental breeding population of tambaqui. Estimation of genetic parameters was performed using a genomic relationship matrix (SNPs data) obtained from an experimental challenge performed in 70 full-sib families. The experimental challenge was successfully performed in three replicate tanks, using the parasite eggs in the ichthyoplankton as source for a natural route of infection, which in turn was induced through oral filtration the plankton. The total gain in body weight of all individuals was measured during the infestation period, as a measure of Resilience (RSF) and averaged 42 g (SD = 21.8). The average parasite abundance per animal at the end of the challenge period, indicating Resistance (RTCT), was about 205.2 parasites (SD = 178.6). The heritability estimates for these traits ranged from 0.17 ± 0.04 to 0.20 ± 0.04, indicating the presence of low to moderate heritability levels for host response against N. buttnerae in tambaqui. Genetic correlations between resistance and resilience traits were consistently negative (favorable) and statistically significant, ranging from −0.512 ± 0.134 to −0.252 ± 0.166. These results suggest the possibility of selecting animals for both resistance and resilience simultaneously. The significant genetic variation found for N. buttnerae resistance and favorable genetic correlations with resilience in tambaqui indicated that selecting superior genotypes is a viable approach to reduce the impact of acanthocephaliasis disease in aquaculture.

Parental selection proposal strategy for recurrent selection in tropical wheat breeding

AbstractRecurrent selection is an effective breeding method for improving complex traits in wheat (Triticum aestivum L.) breeding. In this study, we propose a genitor selection strategy, employing a multi‐trait selection approach and genetic diversity analysis. To evaluate our proposed method, we conducted a lattice design trial during the winter seasons of 2020 and 2021 in Viçosa, MG, Brazil, comprising 87 lines and 13 commercial cultivars. It assessed various traits such as plant height, days to heading, wheat leaf rust, tan spot of wheat, a hundred grain mass, hectoliter weight, and grain yield, and the best linear unbiased predictor (BLUP) was obtained for each trait via restricted maximum likelihood. Next, a genotypic distance matrix, derived from principal component analysis using the BLUP values, was computed to perform hierarchical clustering via the unweighted pair group method with arithmetic mean. The selection of superior genotypes was made utilizing the multi‐trait genotype‐ideotype distance index, resulting in the identification of eight lines and two commercial cultivars as candidates. Furthermore, the genetic diversity analysis revealed distinct clusters among the selected genotypes. To assess the divergence of the chosen genitors, this study proposes a complementarity matrix using factor analysis. Our results indicate that this selection strategy effectively directed the identification of the best and divergent genitors. The complementarity matrix developed in this paper to evaluate the crossings proposal can also be used to evaluate combinations in any panel selected via a multi‐trait approach and can be easily applied and interpreted by breeders of various programs.

Improving predictive ability in sparse testing designs in soybean populations

The availability of high-dimensional genomic data and advancements in genome-based prediction models (GP) have revolutionized and contributed to accelerated genetic gains in soybean breeding programs. GP-based sparse testing is a promising concept that allows increasing the testing capacity of genotypes in environments, of genotypes or environments at a fixed cost, or a substantial reduction of costs at a fixed testing capacity. This study represents the first attempt to implement GP-based sparse testing in soybeans by evaluating different training set compositions going from non-overlapped RILs until almost the other extreme of having same set of genotypes observed across environments for different training set sizes. A total of 1,755 recombinant inbred lines (RILs) tested in nine environments were used in this study. RILs were derived from 39 bi-parental populations of the Soybean Nested Association Mapping (NAM) project. The predictive abilities of various models and training set sizes and compositions were investigated. Training compositions included a range of ratios of overlapping (O-RILs) and non-overlapping (NO-RILs) RILs across environments, as well as a methodology to maximize or minimize the genetic diversity in a fixed-size sample. Reducing the training set size compromised predictive ability in most training set compositions. Overall, maximizing the genetic diversity within the training set and the inclusion of O-RILs increased prediction accuracy given a fixed training set size; however, the most complex model was less affected by these factors. More testing environments in the early stages of the breeding pipeline can provide a more comprehensive assessment of genotype stability and adaptation which are fundamental for the precise selection of superior genotypes adapted to a wide range of environments.

The Genetic Dissection of Economically Important Traits in Chilli Genotypes (Capsicum annuum L.) through Multivariate Analysis

Chilli (Capsicum annuum L.) cultivar share a variety of different and intriguing growth and yield characteristics, for a plant breeder studies on genotypic and phenotypic relationship for horticulture cum vegetable spicy crop and its traits are useful to design, evaluate and to develop selection criteria for desired traits. With this background information the present study focused on identification of crucial characteristics required for boosting yield and to determine the parameters for the selection of superior genotypes. A total of 30 chilli genotypes were subjected to variability, divergence and mutual correlation studies for yield and yield component traits by using multivariate analysis.
 Results from the analysis of variance and variability revealed highly significant differences at (p≤0.01) and (p≤0.05) for all the studied traits. The highest genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) were observed for FL fallowed by FYP, NFP, IFW, WPDM, FD, PH and NSF respectively, except for MC has revealed low GCV and PCV. All the traits were shown the presence of high heritability ( ) in broad sense (>60%) coupled with high GAM (>20%), except for MC, indicating the presence of positive additive gene action and effective transmission of characters to the next generation with selection. Highly significant and positive strong correlation was observed for IFW (r = 0.68**), WPDM (r = 0.54**), TW (r = 0.40*) and FD (r = 0.37*) with FYP, while the path analysis revealed highest direct effect for the traits such as FPT, FL and NFP. Principle component analysis revealed a 70.60% total variation accounted with first four PCAs with Eigen vector values more than one.
 Further cluster analysis grouped the 30 chilli genotypes into four major cluster (Cluster I, II, III and IV) and combined cluster analysis identified genotypes contributing to the maximum variability, viz., cultivars such as LIPSTICK, B.KADDI, B.DABBI, BHOOT JALOKIA, SUM- 17, BCH- 42, PBC- 80, LCA- 310, M- 262, KA2- L, S. SELECTION 1, JCH- 42 and 9608- U, so these genotypes serves as a donor for further breeding programme to develop superior cultivars.

Character Association and Path Co-efficient Analysis Among Inbred Lines of Pearl Millet (Pennisetum glaucum (L.) R. BR.)

A field experiment with 70 pearl millet inbred lines was carried out for analysis of character association and path coefficient for 21 metric traits. A perusal of character association indicated highly significant positive association of panicle weight, green fodder yield plant-1, dry fodder yield plant-1, number of productive tillers plant-1, spike girth, plant height, leaf blade length, number of nodes plant-1, spike length, harvest index, threshing percentage, leaf blade width and specific leaf area at 45 DAS with grain yield plant-1 as well as among themselves at both phenotypic and genotypic levels. Path coefficient analysis indicated that kernel yield plant-1 exhibited high positive direct effect on panicle weight followed by threshing percentage and green fodder yield plant-1. Critical analysis of results obtained from character association and path analysis indicated that grain yield plant-1 had strong positive association with panicle weight which also had high magnitude of positive direct effect. This reveals the importance of this component trait in selection of superior genotypes for higher yield in genotypes of pearl millet.

Assessment of yield performances for grain sorghum varieties by AMMI and GGE biplot analyses

Grain sorghum is an exceptional source of dietary nutrition with outstanding economic values. Breeding of grain sorghum can be slowed down by the occurrence of genotype × environment interactions (GEI) causing biased estimation of yield performance in multi-environments and therefore complicates direct phenotypic selection of superior genotypes. Multi-environment trials by randomized complete block design with three replications were performed on 13 newly developed grain sorghum varieties at seven test locations across China for two years. Additive main effects and multiplicative interaction (AMMI) and genotype + genotype × environment (GGE) biplot models were adopted to uncover GEI patterns and effectively identify high-yielding genotypes with stable performance across environments. Yield (YLD), plant height (PH), days to maturity (DTM), thousand seed weight (TSW), and panicle length (PL) were measured. Statistical analysis showed that target traits were influenced by significant GEI effects (p < 0.001), that broad-sense heritability estimates for these traits varied from 0.40 to 0.94 within the medium to high range, that AMMI and GGE biplot models captured more than 66.3% of total variance suggesting sufficient applicability of both analytic models, and that two genotypes, G3 (Liaoza No.52) and G10 (Jinza 110), were identified as the superior varieties while one genotype, G11 (Jinza 111), was the locally adapted variety. G3 was the most stable variety with highest yielding potential and G10 was second to G3 in average yield and stability whereas G11 had best adaptation only in one test location. We recommend G3 and G10 for the production in Shenyang, Chaoyang, Jinzhou, Jinzhong, Yulin, and Pingliang, while G11 for Yili.

Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets.

In modern plant breeding, genomic selection is becoming the gold standard for selection of superior genotypes. The basis for genomic prediction models is a set of phenotyped lines along with their genotypic profile. With high marker density and linkage disequilibrium (LD) between markers, genotype data in breeding populations tends to exhibit considerable redundancy. Therefore, interest is growing in the use of haplotype blocks to overcome redundancy by summarizing co-inherited features. Moreover, haplotype blocks can help to capture local epistasis caused by interacting loci. Here, we compared genomic prediction methods that either used single SNPs or haplotype blocks with regards to their prediction accuracy for important traits in crop datasets. We used four published datasets from canola, maize, wheat and soybean. Different approaches to construct haplotype blocks were compared, including blocks based on LD, physical distance, number of adjacent markers and the algorithms implemented in the software "Haploview" and "HaploBlocker". The tested prediction methods included Genomic Best Linear Unbiased Prediction (GBLUP), Extended GBLUP to account for additive by additive epistasis (EGBLUP), Bayesian LASSO and Reproducing Kernel Hilbert Space (RKHS) regression. We found improved prediction accuracy in some traits when using haplotype blocks compared to SNP-based predictions, however the magnitude of improvement was very trait- and model-specific. Especially in settings with low marker density, haplotype blocks can improve genomic prediction accuracy. In most cases, physically large haplotype blocks yielded a strong decrease in prediction accuracy. Especially when prediction accuracy varies greatly across different prediction models, prediction based on haplotype blocks can improve prediction accuracy of underperforming models. However, there is no "best" method to build haplotype blocks, since prediction accuracy varied considerably across methods and traits. Hence, criteria used to define haplotype blocks should not be viewed as fixed biological parameters, but rather as hyperparameters that need to be adjusted for every dataset.

Forage peanut genetic variability: Multi-trait selection for forage production and ornamental purposes

The selection of superior genotypes considering several traits simultaneously allows the release of more adapted, productive, and nutritive cultivars. To select forage peanut genotypes for use as animal feed and for ornamental purposes, 67 genotypes were evaluated. Twelve agronomic and nutritive value traits were evaluated in three temporally separated trials: a randomized complete block design. The mixed model method (Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP)) was employed for estimating genetic parameters and predicting genotypic values, which were used in the selection indexes. The selection criteria considered vegetative and seed propagation traits corresponding to the use of forage peanut as animal feed and for ornamental purposes. Seed productivity was also evaluated and correlated with other traits. Genetic variability with high heritability in seed production was observed. Plant vigor, ground cover, and dry matter yield were negatively correlated with seed production. Among the genotypes evaluated, there is a possibility of selecting 14 and 16 genotypes corresponding to seed propagation for animal feed and ornamental purposes, respectively. For vegetative propagation, there are 16 and 14 promising genotypes for animal feed and ornamental purposes, respectively. Vegetatively propagated genotypes generally performed better in terms of agronomic traits related to feed production.

Variability and character association studies for yield and yield contributing characters in cucumber (Cucumis sativus) under low hills of Himachal Pradesh

Cucumber is an important member of family Cucurbitaceae having potential applications across many sectors. Twenty genotypes were evaluated at the Department of Vegetable Science, College of Horticulture and Forestry (Dr Yashwant Singh Parmar University of Horticulture and Forestry), Neri, Hamirpur, Himachal Pradesh during June– September 2021 for studying variability in morphology, yield and its contributing traits. In studying genetic parameters, PDI of downy mildew, number of fruits/plant, total yield per plot and PDI of powdery mildew, traits showed high estimates of PCV and GCV, indicating the considerable amount of variation was present in germplasm. Most of the traits under study showed high heritability with high to moderate genetic advance as a per cent of mean, which showed the influence of additive gene action for controlling traits. Thus, selection is effective for improvement in these cucumber genotypes. Correlation association and path analysis showed fruit length, fruit breadth, internodal length, number of fruits per plant, harvest duration and ascorbic acid. These traits were considered during the selection of superior genotypes among the twenty genotypes. Thus, in this study, LC-C-4-21 and LC-C-14-21 were higher yielders and can be used for further breeding programmes.

Whole-genome resequencing of common bean elite breeding lines

The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing—WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs.

An Analysis of the Correlation between Physiochemical Characteristics of Soil and the Morphological Characteristics of Grewia optiva Drummond in the Northwestern Himalayan Region

Continued research on the physiochemical properties of soil is critical for the long-term maintenance of cropping systems, (including trees), in order to harness their economic benefits. The current study was carried out in the Department of Tree Improvement and Genetic Resources, COF, Nauni, Solan (H.P.) during the period 2020-2023 to quantify the impact of soil nutrient variation on the morphological characteristics of Grewia optiva Drummond in different districts with variable climate and heterogeneous soils. The impacts on growth parameters (tree height, crown spread, leaf traits) of selected populations of Grewia optiva Drummond statistically analyzed using Karl Pearson correlation coefficient. Two composite soil samples representative of the different populations were drawn from the two depths i.e., 0-15 cm (surface layer) and 15-30 cm (subsurface layer). These samples were collected underneath the selected populations of Grewia optiva Drummond. The collected soil samples were tested using standard soil methods and results were analysed using OPSTAT software. There was highly positive correlation observed between leaf area and soil N (0.509), leaf area and SOC (0.407), leaf area and soil P (0.728) and leaf area and soil K (0.577). Leaf length showed a highly significant correlation with SOC (0.401), soil N (0.509), soil P (0.710), and soil K (0.592). The tree height (0.385), tree diameter (0.602), crown spread (N-S) (0.629), crown spread (E-W) (0.334), branch nodal length (0.436) and leaf width (0.470) showed a significant positive correlation with soil P. Soil K showed a significant positive correlation with tree height (0.774), tree diameter (0.645), crown spread (N-S) (0.576), crown spread (E-W) (0.314), branch nodal length (0.737) and leaf width (0.592). Soil pH demonstrated highly significant correlation with Leaf width (0.449). The correlation developed between tree morphological and soil characteristics will help in quantify the impact of different soil characteristics on tree and leaf morphometric characteristics. It will further help in identification and selection of superior genotypes of Grewia optiva for further propagation to get improved genetic gain and for production of quality planting material.

Increased Zygote-Derived Plantlet Formation through In Vitro Rescue of Immature Embryos of Highly Apomictic Opuntia ficus-indica (Cactaceae).

O. ficus-indica (prickly pear cactus) is an important forage and food source in arid and semiarid ecosystems and is the most important cactus species in cultivation globally. The high degree of apomixis in the species is a hindrance in plant breeding programs where genetic segregation is sought for the selection of superior genotypes. To understand if in ovulo embryo rescue could increase the proportion of zygotic seedlings, we compared the mature seed-derived seedlings with those regenerated from in vitro embryo rescue at 20, 25, 30, 35, and 40 post-anthesis days (PADs) in four Italian cultivars. The seedlings were classified as apomictic or zygotic based on molecular marker analysis using inter-sequence single repeat (ISSR) primers. Multiple embryos were recovered from all the cultured immature ovules, and plantlets were regenerated and acclimatized to the field post hardening, with success rates ranging from 62% ('Senza spine') to 83% ('Gialla'). The level of polyembryony differed among cultivars and recovery dates, with the highest being 'Rossa', producing 4.8 embryos/ovule at 35 PADs, and 'Gialla', the lowest, with 2.7 at 40 PADs. The maximum number of embryos observed within a single ovule was 14 in 'Trunzara bianca'. ISSR analysis revealed that ovule culture at 35 PADs produced the highest percentage of zygotic seedlings in all the cultivars, from 51% ('Rossa') to 98% ('Gialla'), with a high genotype effect as well. Mature seeds produced much fewer seedlings per seed, ranging from 1.2 in 'Trunzara bianca' to 2.0 in 'Rossa' and a lower percentage of zygotic seedlings (from 14% in 'Rossa' to 63% in 'Gialla'). Our research opens a pathway to increase the availability of zygotic seedlings in O. ficus-indica breeding programs through in ovulo embryo culture.

Phenotyping of architecture traits of loblolly pine trees using stereo machine vision and deep learning: Stem diameter, branch angle, and branch diameter

Loblolly pine is one of the most planted forest tree species in the Southern United States for sawtimber production. The sawtimber yield potential of a pine tree is significantly impacted by its stem and branch architecture, which is of important focus in tree improvement programs. However, phenotyping these traits in the upper crown of pine trees is currently based on subjective visual assessments. This study investigated the feasibility of quantifying stem diameter, branch angle, and branch diameter of six-year-old loblolly pine trees in a progeny test using stereo 3D imaging, deep learning-based instance segmentation, and image and point cloud processing techniques. Instance segmentation of branches and stems was performed as well as principal component analysis (PCA) in 2D images, followed by 3D reconstruction of the segmented organs. The resulting 3D point clouds were further processed using random sample consensus (RANSAC) and statistical outlier removal to extract stem diameter, branch angle, and branch diameter. When compared to the manual ground-truth measurements, the three system-derived parameters achieved RMSEs of 0.055 m, 5.0˚, and 5.6 mm, respectively. In addition, Bland-Altman analyses showed that the stem diameter and branch angle estimations were found with limits of agreement of±0.098 m and±9.8˚, respectively, with nonsignificant biases. On the other hand, branch diameter estimation showed −12.1 mm and 9.3 mm for lower and upper limits of agreement with a bias. The proposed system demonstrates promising potential as a high-throughput low-cost precision phenotyping tool for the characterization of loblolly pine tree architecture under field conditions, facilitating the selection of superior genotypes with improved sawtimber properties.

Estimation of genetic variation in yield, its contributing characters and capsaicin content of Capsicum chinense Jacq. (ghost pepper) germplasm from Northeast India.

Capsicum chinense Jacq. (ghost pepper), a naturally occurring chili species of Northeast India is known throughout the world for its high pungency and a pleasant aroma. The economic importance is due to the high capsaicinoid levels, the main source for pharmaceutical industries. The present study focused on identifying important traits necessary for increasing the yield and pungency of ghost pepper and to determine the parameters for the selection of superior genotypes. A total of 120 genotypes with more than 1.2% capsaicin content (>1,92,000 Scoville Heat Unit, w/w on dry weight basis) collected from different northeast Indian regions were subjected to variability, divergence and correlation studies. Levene's homogeneity test of variance studied for three environments did not show significant deviation and so homogeneity of variance was reasonably met for analysis of variance study. Genotypic and phenotypic coefficient of variation was highest for fruit yield per plant (33.702, 36.200, respectively), followed by number of fruits per plant (29.583, 33.014, respectively) and capsaicin content (25.283, 26.362, respectively). The trait number of fruits per plant had maximum direct contribution to fruit yield per plant and the trait fruit yield per plant towards capsaicin content in the correlation study. High heritability with high genetic advance, which is the most favored selection criteria was observed for fruit yield per plant, number of fruits per plant, capsaicin content, fruit length and fruit girth. The genetic divergence study partitioned the genotypes into 20 clusters, where fruit yield per plant contributed maximum towards total divergence. Principal components analysis (PCA) studied to determine the largest contributor of variation showed 73.48% of the total variability, of which the PC1 and PC2 contributed 34.59% and 16.81% respectively.

Genome-wide association study of multiyear dynamic growth traits in hybrid Liriodendron identifies robust genetic loci associated with growth trajectories.

The genetic factors underlying growth traits differ over time points or stages. However, most current studies of phenotypes at single time points do not capture all loci or explain the genetic differences underlying growth trajectories. Hybrid Liriodendron exhibits obvious heterosis and is widely cultivated, although its complex genetic mechanism underlying growth traits remains unknown. A genome-wide association study (GWAS) is an effective method for elucidating the genetic architecture by identifying genetic loci underlying complex quantitative traits. In the present study, using a GWAS, we identified robust loci associated with growth trajectories in hybrid Liriodendron populations. We selected 233 hybrid progenies derived from 25 crosses for resequencing, and measured their tree height (H) and diameter at breast height (DBH) for 11 consecutive years; 192 972 high-quality single nucleotide polymorphisms (SNPs) were obtained. The dynamics of the multiyear single-trait GWAS showed that year-specific SNPs predominated, and only five robust SNPs for DBH were identified in at least three different years. Multitrait GWAS analysis with model parameters as latent variables also revealed 62 SNPs for H and 52 for DBH associated with the growth trajectory, displaying different biomass accumulation patterns, among which four SNPs exerted pleiotropic effects. All identified SNPs also exhibited temporal variations in effect sizes and inheritance patterns potentially related to different growth and developmental stages. The haplotypes resulting from these significant SNPs might pyramid favorable loci, benefitting the selection of superior genotypes. The present study provides insights into the genetic architecture of dynamic growth traits and lays a basis for future molecular-assisted breeding.

Multitrait selection in seedless grape hybrids in semiarid regions of Brazil

AbstractThe absence of seeds has been one of the most valued traits in grapes (Vitis spp.) for fresh consumption. However, the simultaneous selection of superior genotypes for multiple traits is complex. The objective of this study was to select genotypes of superior seedless table grapes in semiarid regions of Brazil. Multiple traits were considered by using the factor analysis and genotype–ideotype best linear unbiased prediction (FAI‐BLUP) selection index. A total of 110 grape progenies from 24 crosses were evaluated for traits of agronomic interest. Each hybrid was represented by a single vine plant, without experimental design or repetition. The mixed‐model methodology was used to predict the breeding values. The FAI‐BLUP index was used to select superior genotypes based on factor analysis and the genotype–ideotype distance. Four factors explained the 11 characteristics studied, with a variability of 81.84%. Desirable gains were observed for 10 of the 11 traits evaluated. The FAI‐BLUP index allowed the selection of superior seedless table grape hybrids, which can be used in the genetic improvement of grapevines. In conclusion, we report the selection of seedless table grape hybrids for our study to advance in the table grape breeding program in Brazilian semiarid regions.

Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions.

Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.