Genetic Correlation for Pre-Weaning and Post-Weaning Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

The aim of this study was to estimate genetic, environmental and phenotypic correlation between birth weight (BW) and weight at 205 days age (W205), BW and weight at 365 days age (W365) and W205-W365, using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data that included 3,883 observations from Mediterranean breed buffaloes. With the purpose to estimate variance and covariance, bivariate analyses were performed using Gibbs sampler that is included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, maternal environmental random effect and contemporary group as fixed effect. The convergence diagnosis was achieved using Geweke, a method that uses an algorithm implemented in R software through the package Bayesian Output Analysis. The calculated direct genetic correlations were 0.34 (BW-W205), 0.25 (BW-W365) and 0.74 (W205-W365). The environmental correlations were 0.12, 0.11 and 0.72 between BW-W205, BW-W365 and W205-W365, respectively. The phenotypic correlations were low for BW-W205 (0.01) and BW-W365 (0.04), differently than the obtained for W205-W365 with a value of 0.67. The results indicate that BW trait have low genetic, environmental and phenotypic association with the two others traits. The genetic correlation between W205 and W365 was high and suggests that the selection for weight at around 205 days could be beneficial to accelerate the genetic gain.

Genetic Parameters for Growth Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

Quantitative analysis of growth genetic parameters is not available for many breeds of buffaloes making selection and breeding decisions an empirical process that lacks robustness. The objective of this study was to estimate heritability for birth weight (BW), weight at 205 days (W205) and 365 days (W365) of age using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data. For the traits BW, W205 and W365 of Brazilian Mediterranean buffaloes 5169, 3792 and 3883 observations have been employed for the analysis, respectively. In order to obtain the estimates of variance, univariate analyses were conducted using the Gibbs sampler included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, random maternal permanent environmental effect and contemporary group that was treated as a fixed effect. The convergence diagnosis was performed employing Geweke, a method that uses an algorithm from the Bayesian Output Analysis package that was implemented using R software environment. The average values for weight traits were 37.6 +/- 4.7 kg for BW, 192.7 +/- 40.3 kg for W205 and 298.6 +/- 67.4 kg for W365. The heritability posterior distributions for direct and maternal effects were symmetric and close to those expected in a normal distribution. Direct heritability estimates obtained using the modes were 0.30 (BW), 0.52 (W205) and 0.54 (W365). The maternal heritability coefficient estimates were 0.31, 0.19 and 0.21 for BW, W205 and W365, respectively. Our data suggests that all growth traits and mainly W205 and W365, have clear potential for yield improvement through direct genetic selection.

Genetic Parameters for Milk Yield and Lactation Length of Crossbred Buffaloes from Brazil by Bayesian Inference

The objective of the study was to estimate heritability and repeatability for milk yield (MY) and lactation length (LL) in buffaloes using Bayesian inference. The Brazilian genetic improvement program of buffalo provided the data that included 628 females, from four herds, born between 1980 and 2003. In order to obtain the estimates of variance, univariate analyses were performed with the Gibbs sampler, using the MTGSAM software. The model for MY and LL included direct genetic additive and permanent environment as random effects, and contemporary groups, milking frequency and calving number as fixed effects. The convergence diagnosis was performed with the Geweke method using an algorithm implemented in R software through the package Bayesian Output Analysis. Average for milk yield and lactation length was 1,546.1 +/- 483.8 kg and 252.3 +/- 42.5 days, respectively. The heritability coefficients were 0.31 (mode), 0.35 (mean) and 0.34 (median) for MY and 0.11 (mode), 0.10 (mean) and 0.10 (median) for LL. The repeatability coefficient (mode) were 0.50 and 0.15 for MY and LL, respectively. Milk yield is the only trait with clear potential for genetic improvement by direct genetic selection. The repeatability for MY indicates that selection based on the first lactation could contribute for an improvement in this trait.

Genetic relationship among reproductive traits in Nellore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic analysis for gestation length, birth weight, weaning weight, and accumulated productivity in Nellore beef cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic and phenotypic parameters of carcass and organ traits of broiler chickens

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic characterization of fig tree mutants with molecular markers

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes.

Genetic transformation of three sweet orange cultivars from explants of adult plants

The difficulty in adult tissue genetic transformation in woody species is still an obstacle to be overcome, including in most sweet orange cultivars of the Brazilian citrus industry. This work reports that, after in vitro culture adjustments, transgenic adventitious buds of 'Hamlin', 'Pra', and 'Valencia' sweet oranges (Citrus sinensis L. Osbeck) were recovered using adult material as explant source, in genetic transformation experiments via Agrobacterium tumefaciens. The transgenic buds were identified by the GUS histochemical analysis and confirmed by PCR analysis, which indicated the presence of an amplified fragment of 817 bp corresponding to the uidA gene sequence. The efficiencies of genetic transformation for 'Hamlin', 'Pra', and 'Valencia' sweet orange cultivars were 2.5, 1.4, and 3.7%, respectively. Media supplemented with auxins and cytokinins during co-culture, and media with high concentrations of cytokinins (3 mg L-1) during transgenic selection led to the transformation and, consequently, the regeneration of adequate number of adventitious buds for the three cultivars. The use of sonication during the explant disinfection was not effective to reduce endophytic contamination and reduced transformation efficiency.

Genetic relationship between growth and reproductive traits in Nellore cattle

The objective of this study was to evaluate the genetic relationship between postweaning weight gain (PWG), heifer pregnancy (HP), scrotal circumference (SC) at 18 months of age, stayability at 6 years of age (STAY) and finishing visual score at 18 months of age (PREC), and to determine the potential of these traits as selection criteria for the genetic improvement of growth and reproduction in Nellore cattle. The HP was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 days. The STAY was defined as whether or not a cow calved every year up to the age of 6 years, given that she was provided the opportunity to breed. The Bayesian linear-threshold analysis via the Gibbs sampler was used to estimate the variance and covariance components applying a multitrait model. Posterior mean estimates of direct heritability were 0.15 +/- 0.00, 0.42 +/- 0.02, 0.49 +/- 0.01, 0.11 +/- 0.01 and 0.19 +/- 0.00 for PWG, HP, SC, STAY and PREC, respectively. The genetic correlations between traits ranged from 0.17 to 0.62. The traits studied generally have potential for use as selection criteria in genetic breeding programs. The genetic correlations between all traits show that selection for one of these traits does not imply the loss of the others.

Genetic basis of variation for root traits and response to heat stress in durum wheat

Durum wheat is the second most important wheat species worldwide and the most important crop in several Mediterranean countries including Italy. Durum wheat is primarily grown under rainfed conditions where episodes of drought and heat stress are major factors limiting grain yield. The research presented in this thesis aimed at the identification of traits and genes that underlie root system architecture (RSA) and tolerance to heat stress in durum wheat, in order to eventually contribute to the genetic improvement of this species. In the first two experiments we aimed at the identification of QTLs for root trait architecture at the seedling level by studying a bi-parental population of 176 recombinant inbred lines (from the cross Meridiano x Claudio) and a collection of 183 durum elite accessions. Forty-eight novel QTLs for RSA traits were identified in each of the two experiments, by means of linkage- and association mapping-based QTL analysis, respectively. Important QTLs controlling the angle of root growth in the seedling were identified. In a third experiment, we investigated the phenotypic variation of root anatomical traits by means of microscope-based analysis of root cross sections in 10 elite durum cultivars. The results showed the presence of sizeable genetic variation in aerenchyma-related traits, prompting for additional studies aimed at mapping the QTLs governing such variation and to test the role of aerenchyma in the adaptive response to abiotic stresses. In the fourth experiment, an association mapping experiment for cell membrane stability at the seedling stage (as a proxy trait for heat tolerance) was carried out by means of association mapping. A total of 34 QTLs (including five major ones), were detected. Our study provides information on QTLs for root architecture and heat tolerance which could potentially be considered in durum wheat breeding programs.

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.

Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter]

Tef Eragrostis tef (Zucc.) Trotter is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n=4x=40), belongs to the Family Poaceae and, together with finger millet (Eleusine coracana Gaertn), to the Subfamily Chloridoideae. It was believed to have originated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

Genetic diversity revealed in the apomictic fruit species Garcinia mangostana L. (mangosteen)

The novel molecular marker technique Randomly Amplified DNA Fingerprinting (RAF) was used to survey genetic relationships between 37 accessions of the tropical fruit G. mangostana (mangosteen) and among 11 accessions from eight other Garcinia species. Although mangosteen is believed to reproduce exclusively through apomixis, our results show that considerable genetic diversity exists within G. mangostana and between other Garcinia species. Among the 37 G. mangostana accessions examined, nine different genotypes were identified which clustered into three distinct groups based on correspondence analysis (reciprocal averaging). For 26 (70%) of the accessions no marker variation was detected over 530 loci screened. A further eight (22%) accessions exhibited very low levels of variation (0.2-1%) suggesting at least one well conservedm angosteen genotype. The remaining three accessions (8%) showed extensive variation (22-31%) compared with the majority of accessions. The three mangosteen groups were 63-70% dissimilar to the other Garcinia species investigated. The genetic diversity identified in this research will assist in the conservation of Garcinia germplasm and provides a valuable framework for the genetic improvement of mangosteen.

Genetic variation in growth and wood-quality traits of Corymbia citriodora subsp. variegata across three sites in south-east Queensland, Australia

Ten growth or wood-quality traits were assessed in three nearby Corymbia citriodora subsp. variegata (CCV) open-pollinated family-within-provenance trials (18 provenances represented by a total of 374 families) to provide information for the development of a breeding program targeting both pulp and solid-wood products. Growth traits (diameter at breast high over bark [DBH], height and conical volume) were assessed at 3 and 7 years of age. Wood-quality traits (density [DEN], Kraft pulp yield [KPY], modulus of elasticity [MoE] and microfibril angle [MfA]) were predicted using near-infrared spectroscopy on wood samples collected from these trials when aged between 10 and 12 years. The high average KPY, DEN and MoE, and low average MfA observed indicates CCV is very suitable for both pulp and timber products. All traits were under moderate to strong genetic control. In across- trials analyses, high (>0.4) heritability estimates were observed for height, DEN, MoE and MfA, while moderate heritability estimates (0.24 to 0.34) were observed for DBH, volume and KPY. Most traits showed very low levels of genotype × site interaction. Estimated age–age genetic correlations for growth traits were strong at both the family (0.97) and provenance (0.99) levels. Relationships among traits (additive genetic correlation estimates) were favourable, with strong and positive estimates between growth traits (0.84 to 0.98), moderate and positive values between growth and wood-quality traits (0.32 to 0.68), moderate and positive between KPY and MoE (0.64), and high and positive between DEN and MoE (0.82). However, negative (but favourable) correlations were detected between MfA and all other evaluated traits (−0.31 to −0.96). The genetic correlation between the same trait expressed on two different sites, at family level, ranged from 0.24 to 0.42 for growth traits, and from 0.29 to 0.53 for wood traits. Therefore simultaneous genetic improvement of growth and wood property traits in CCV for the target environment in south-east Queensland should be possible, given the moderate to high estimates of heritability and favourable correlations amongst all traits studied, unless genotype × site interactions are greater than was evident. © 2016 NISC (Pty) Ltd

Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.