Genome selection in fruit breeding: application to table grapes.

Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant to dagger nematode and Pierce?s disease (PD), and ?B90-116?, a susceptible Vitis vinifera cultivar with desirable fruit characteristics. Our aim was to enhance the knowledge on the genomic variation of agronomical traits in table grape populations for future use in marker-assisted selection (MAS) and GS, by discovering a set of molecular markers associated with genomic regions involved in this variation. A number of Quantitative Trait Loci (QTL) were discovered but this method is inaccurate and the genetic architecture of the studied population was better captured by the BLasso method of genomic selection, which allowed for efficient inference about the genetic contribution of the various marker loci. The technology of genomic selection afforded greater efficiency than QTL analysis and can be very useful in speeding up the selection procedures for agronomic traits in table grapes.

Marker-assisted selection integrated to the embrapa common bean breeding program.

The establishment of a specific Marker-Assisted Selection Facility at the Embrapa Rice and Beans Biotechnology Laboratory, in 2014, has better supported the routine analysis with molecular markers demanded by the Embrapa Common Bean Breeding Program. In addition, it has also supported other Embrapa plant breeding programs, such as rice and cotton.

Genetic diversity of mango accessions (Mangifera indica) using new microsatellite markers and morphological descriptors.

Genetic diversity estimates based on morphological and molecular data can provide different information on the relationship between cultivars of a species. This study aimed to develop new microsatellite markers as additional tools in genetic studies on mangoes (Mangifera indica L.), and to analyze the genetic variability of 20 mango cultivars based on morphological descriptors and microsatellite markers. We aimed to better understand the cultivars enhanced breeding histories and to support crossbreeding planning. Positive clones were selected from a DNA library enriched for microsatellite regions for sequencing and primer design. Four plants of each of the 20 accessions were used for observations, based on 48 morphological descriptors. Twenty accessions were analyzed using 27 microsatellite markers, of which 16 were developed during this study. The clusters, based on the morphological descriptors by Ward - MLM strategy and the microsatellite markers, suggested that Brazilian mango cultivars have extensive genetic diversity and are related to cultivars with different provenances, demonstrating their different enhanced breeding histories.

Genomic structure and marker-derived gene networks for growth and meat quality traits of brazilian nelore beef cattle.

Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.

Novel and highly informative Capsicum SSR markers and their cross-species transferability.

2016

Mapping highly informative SSR markers in the genome of Magnaportheoryzae from wheat.

2016