Temporal and genomic analysis of additive genetic variance in breeding programmes

Genetic variance is a central parameter in quantitative genetics and breeding. Assessing changes in genetic variance over time as well as the genome is therefore of high interest. Here, we extend a previously proposed framework for temporal analysis of genetic variance using the pedigree-based model, to a new framework for temporal and genomic analysis of genetic variance using marker-based models. To this end, we describe the theory of partitioning genetic variance into genic variance and within-chromosome and between-chromosome linkage-disequilibrium, and how to estimate these variance components from a marker-based model fitted to observed phenotype and marker data. The new framework involves three steps: (i) fitting a marker-based model to data, (ii) sampling realisations of marker effects from the fitted model and for each sample calculating realisations of genetic values and (iii) calculating the variance of sampled genetic values by time and genome partitions. Analysing time partitions indicates breeding programme sustainability, while analysing genome partitions indicates contributions from chromosomes and chromosome pairs and linkage-disequilibrium. We demonstrate the framework with a simulated breeding programme involving a complex trait. Results show good concordance between simulated and estimated variances, provided that the fitted model is capturing genetic complexity of a trait. We observe a reduction of genetic variance due to selection and drift changing allele frequencies, and due to selection inducing negative linkage-disequilibrium.

A Review of Omics Technologies and Bioinformatics to Accelerate Improvement of Papaya Traits

Papaya (Carica papaya) is an economically important fruit crop that is mostly planted in tropical and subtropical regions. Major diseases of papaya, such as the papaya dieback disease (PDD), papaya ringspot virus (PRSV) disease, and papaya sticky disease (PSD), have caused large yield and economic losses in papaya-producing countries worldwide. Postharvest losses have also contributed to the decline in papaya production. Hence, there is an urgent need to secure the production of papaya for a growing world population. Integration of omics resources in crop breeding is anticipated in order to facilitate better-designed crops in the breeding programme. In papaya research, the application of omics and bioinformatics approaches are gradually increased and are underway. Hence, this review focuses on addressing omics technologies and bioinformatics that are used in papaya research. To date, four traits of the papaya have been studied using omics and bioinformatics approaches, which include its ripening process, abiotic stress, disease resistance, and fruit quality (i.e., sweetness, fruit shape, and fruit size). This review also highlights the potential of genetics and genomics data, as well as the systems biology approach that can be applied in a papaya-breeding programme in the near future.

Over 50 Years of Potato Parental Line Breeding Programme at the Plant Breeding and Acclimatization Institute in Poland

The paper describes the potato parental line breeding programme developed in Poland from the 1960s. The aim of the programme was to create parental forms useful for speeding up the breeding of new potato varieties and getting higher efficiency in directed selection for desired traits. The programme introduced new sources of resistance and quality traits into the Polish breeding pool by conducting research and breeding of tetraploid and diploid parental lines. The programme had significant impact on potato breeding, with 72 Polish potato varieties originating from crossings involving parental lines. These varieties show higher levels of resistance to major pathogens of potato crops, including resistance to Potato virus Y and late blight in starch group. Besides the direct impact on potato breeding, the programme was the stimulus for developing studies focused on potato genotype.

Nature and Magnitude of Genetic Divergence among Blackgram [Vigna mungo (L.) Hepper] Genotypes

Background: The choice of parents is a very crucial step which decides the success or failure of any plant breeding programme. Using the diversity analysis, parents with high diversity can be chosen to generate high magnitude of useful variability. Therefore, the present investigation was planned to assess the genetic divergence among 100 genotypes of blackgram for identification of diverse genotypes for their utilization in breeding programme.Methods: The material for study consisted of 100 blackgram genotypes collected from different sources and were evaluated at ARS, Bidar during kharif-2018. The experimental trial was laid out in lattice design (10×10) with two replications. Observations on 12 quantitative characters. The genetic divergence was assessed by using Mahalanobis’ generalized distance (D2) and clustering of genotypes by Tocher’s method.Result: The relative contribution of each character to the total diversity was different and contribution of days to maturity was maximum (66.04%) followed by reproductive period (15.86%). The genotypes were grouped into nine clusters by Tocher’s method. The cluster pattern revealed that, cluster II was the largest with 28 genotypes followed by cluster I (26), V (19), III (11), IV (10) and VII (3) and remaining viz., VI, VIII and IX were solitary clusters. The inter-cluster distance ranged from 15.50 to 514.44 indicating high magnitude of diversity. The genotypes belonging to cluster III viz., BDU-20, BDU-3-20, BDU-68, TRCRU-22 possessed desirable traits like earliness and higher seed size and genotypes of cluster IV viz., BDU-9, BDU-10, LBG-752 possessed traits like higher reproductive period, maturity and high seed yield were identified as diverse. These genotypes could be involved in recombination breeding programme for the improvement productivity in blackgram.