DNA banking for plant breeding, biotechnology and biodiversity evaluation.

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.

Spatial statistical analysis and selection of genotypes in plant breeding

The objective of this study was to evaluate the efficiency of spatial statistical analysis in the selection of genotypes in a plant breeding program and, particularly, to demonstrate the benefits of the approach when experimental observations are not spatially independent. The basic material of this study was a yield trial of soybean lines, with five check varieties (of fixed effect) and 110 test lines (of random effects), in an augmented block design. The spatial analysis used a random field linear model (RFML), with a covariance function estimated from the residuals of the analysis considering independent errors. Results showed a residual autocorrelation of significant magnitude and extension (range), which allowed a better discrimination among genotypes (increase of the power of statistical tests, reduction in the standard errors of estimates and predictors, and a greater amplitude of predictor values) when the spatial analysis was applied. Furthermore, the spatial analysis led to a different ranking of the genetic materials, in comparison with the non-spatial analysis, and a selection less influenced by local variation effects was obtained.

Designs and model effects definitions in the initial stage of a plant breeding program

The objective of this work was to compare the relative efficiency of initial selection and genetic parameter estimation, using augmented blocks design (ABD), augmented blocks twice replicated design (DABD) and group of randomised block design experiments with common treatments (ERBCT), by simulations, considering fixed effect model and mixed model with regular treatment effects as random. For the simulations, eight different conditions (scenarios) were considered. From the 600 simulations in each scenario, the mean percentage selection coincidence, the Pearsons´s correlation estimates between adjusted means for the fixed effects model, and the heritability estimates for the mixed model were evaluated. DABD and ERBCT were very similar in their comparisons and slightly superior to ABD. Considering the initial stages of selection in a plant breeding program, ABD is a good alternative for selecting superior genotypes, although none of the designs had been effective to estimate heritability in all the different scenarios evaluated.

Microsatellites for genetic studies and breeding programs in common bean

Twenty microsatelitte loci were identified and characterized in common bean. Microsatellites were tested in 14 genotypes. The allele number ranged from 1 to 3, and the polymorphism information content (PIC) was between 0.14 and 0.65. These polymorphic markers are available to be used for breeding programs.

Root traits of common bean genotypes used in breeding programs for disease resistance

The objective of this work was to assess root traits of 19 common bean genotypes, used in breeding programs for disease resistance. Genotypes DOR 364 and G 19833 were used as deep and shallow basal root checks, respectively. The number of whorls and basal roots were assessed on five-day old seedlings grown in germination paper. Growth pouch studies were conducted to evaluate basal root gravitropism and lateral root length from primary roots, in seven-day old seedlings. The following root gravitropic traits were estimated: basal growth angle, shallow basal root length (localized in the top 2 cm), and relative shallow basal root growth. Number of whorls varied from 1.47 to 3.07, and number of basal roots ranged from 5.67 (genotype TO) to 12.07 (cultivar Jalo MG-65). Cultivars BRS MG Talismã, Carioca, BRS Pioneiro, and Diamante Negro exhibited shallow basal roots, while genotypes Vi-10-2-1, TU, AB 136, and México 54 showed deep basal roots. Cultivar Jalo MG-65 showed more lateral roots from the primary root than the other genotypes. Genotypes used on common bean breeding programs for disease resistance have great variability on basal and primary root traits.

Tolerance to preharvest sprouting and yield of wheat genotypes from different breeding programs

Abstract:The objective of this work was to characterize the performance of elite wheat genotypes from different Brazilian breeding programs for traits associated with grain yield and preharvest sprouting. The study was conducted in 2010 and 2011 in the municipality of Capão do Leão, in the state of Rio Grande do Sul, Brazil, in a randomized complete block design with three replicates. Thirty-three wheat genotypes were evaluated for traits related to preharvest sprouting and grain yield. The estimate of genetic distance was used to predict potential combinations for selection of plants with high grain yield and tolerance to preharvest sprouting. The combined analysis of sprouted grains and falling number shows that the TBIO Alvorada, TBIO Mestre, Frontana, Fundacep Raízes, Fundacep Cristalino, and BRS Guamirim genotypes are tolerant to preharvest sprouting. Combinations of TBIO Alvorada and TBIO Mestre with Fundacep Cristalino show high potential for recovering superior genotypes for high grain yield and tolerance to preharvest sprouting.

Screening and HPLC methods for carotenoids in sweetpotato, cassava and maize for plant breeding trials

Analytical methods for sweetpotato, cassava and maize were developed. In orange and salmon-fleshed sweetpotatoes, (all-E)-beta-carotene predominated and results of spectrophotometric screening and HPLC quantification did not differ significantly. In yellow-fleshed sweetpotato and cassava, however, spectrophotometric screening overestimated the HPLC values because of the presence of several minor carotenoids. Aside from (all-E)-beta-carotene, Z-isomers were present in cassava in appreciable amounts. For both crops, extraction with acetone or tetrahydrofuran: methanol. (1: 1), using a mortar and pestle or a Polytron homogenizer, gave equivalent results. Rehydration of dry maize at room temperature for 30 min or at 85 degrees C for 5, 10 or 15 min gave equivalent results. Concentrations obtained with the C18 and C30 columns did not differ significantly for zeaxanthin, lutein, beta-cryptoxanthin and beta-carotene in the all-E-configuration, but their Z-isomers were difficult to locate in the chromatogram obtained with the C30 column. Extraction with tetrahydrofuran:methanol (1:1) gave significantly lower results for zeaxanthin and lutein. (c) 2005 Elsevier Ltd. All rights reserved.

Strategies to improve the efficiency of genomic selection in animal breeding programs

Pós-graduação em Zootecnia - FCAV

Comparison of genetic gains per year for carcass traits among breeding programs in the Japanese Brown and the Japanese Black cattle

The breeding program for beef cattle in Japan has changed dramatically over 4 decades. Visual judging was done initially, but progeny testing in test stations began in 1968. In the 1980s, the genetic evaluation program using field records, so-called on-farm progeny testing, was first adopted in Oita, Hyogo, and Kumamoto prefectures. In this study, genetic trends for carcass traits in these 3 Wagyu populations were estimated, and genetic gains per year were compared among the 3 different beef cattle breeding programs. The field carcass records used were collected between 1988 and 2003. The traits analyzed were carcass weight, LM area, rib thickness, s.c. fat thickness, and beef marbling standard number. The average breeding values of reproducing dams born the same year were used to estimate the genetic trends for the carcass traits. For comparison of the 3 breeding programs, birth years of the dams were divided into 3 periods reflecting each program. Positive genetic trends for beef marbling standard number were clearly shown in all populations. The genetic gains per year for all carcass traits were significantly enhanced by adopting the on-farm progeny testing program. These results indicate that the on-farm progeny testing program with BLUP is a very powerful approach for genetic improvement of carcass traits in Japanese Wagyu beef cattle.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.