A marker-assisted backcross approach for developing submergence-tolerant rice cultivars

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC2F2 generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC3F2 double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3-3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program.

Quantitative trait loci detection and benefits from marker-assisted selection in dairy cattle

Knowing the chromosomal areas or actual genes affecting the traits under selection would add more information to be used in the selection decisions which would potentially lead to higher genetic response. The first objective of this study was to map quantitative trait loci (QTL) affecting economically important traits in the Finnish Ayrshire population. The second objective was to investigate the effects of using QTL information in marker-assisted selection (MAS) on the genetic response and the linkage disequilibrium between the different parts of the genome. Whole genome scans were carried out on a grand-daughter design with 12 half-sib families and a total of 493 sons. Twelve different traits were studied: milk yield, protein yield, protein content, fat yield, fat content, somatic cell score (SCS), mastitis treatments, other veterinary treatments, days open, fertility treatments, non-return rate, and calf mortality. The average spacing of the typed markers was 20 cM with 2 to 14 markers per chromosome. Associations between markers and traits were analyzed with multiple marker regression. Significance was determined by permutation and genome-wise P-values obtained by Bonferroni correction. The benefits from MAS were investigated by simulation: a conventional progeny testing scheme was compared to a scheme where QTL information was used within families to select among full-sibs in the male path. Two QTL on different chromosomes were modelled. The effects of different starting frequencies of the favourable alleles and different size of the QTL effects were evaluated. A large number of QTL, 48 in total, were detected at 5% or higher chromosome-wise significance. QTL for milk production were found on 8 chromosomes, for SCS on 6, for mastitis treatments on 1, for other veterinary treatments on 5, for days open on 7, for fertility treatments on 7, for calf mortality on 6, and for non-return rate on 2 chromosomes. In the simulation study the total genetic response was faster with MAS than with conventional selection and the advantage of MAS persisted over the studied generations. The rate of response and the difference between the selection schemes reflected clearly the changes in allele frequencies of the favourable QTL. The disequilibrium between the polygenes and QTL was always negative and it was larger with larger QTL size. The disequilibrium between the two QTL was larger with QTL of large effect and it was somewhat larger with MAS for scenarios with starting frequencies below 0.5 for QTL of moderate size and below 0.3 for large QTL. In conclusion, several QTL affecting economically important traits of dairy cattle were detected. Further studies are needed to verify these QTL, check their presence in the present breeding population, look for pleiotropy and fine map the most interesting QTL regions. The results of the simulation studies show that using MAS together with embryo transfer to pre-select young bulls within families is a useful approach to increase the genetic merit of the AI-bulls compared to conventional selection.

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.” Abstract Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Potential applications of reproductive and molecular genetic technologies in the selective breeding of aquaculture species

The use of reproductive and genetic technologies can increase the efficiency of selective breeding programs for aquaculture species. Four technologies are considered, namely: marker-assisted selection, DNA fingerprinting, in-vitro fertilization, and cryopreservation. Marker-assisted selection can result in greater genetic gain, particularly for traits difficult or expensive to measure, than conventional selection methods, but its application is currently limited by lack of high density linkage maps and by the high cost of genotyping. DNA fingerprinting is most useful for genetic tagging and parentage verification. Both in-vitro fertilization and cryopreservation techniques can increase the accuracy of selection while controlling accumulation of inbreeding in long-term selection programs. Currently, the cost associated with the utilization of reproductive and genetic techniques is possibly the most important factor limiting their use in genetic improvement programs for aquatic species.

Perspectives from agriculture: advances in livestock breeding - implications for aquaculture genetics

In this paper we present livestock breeding developments that could be taken into consideration in the genetic improvement of farmed aquaculture species, especially in freshwater fish. Firstly, the current breeding objective in aquatic species has focused almost exclusively on the improvement of body weight at harvest or on growth related traits. This is unlikely to be sufficient to meet the future needs of the aquaculture industry. To meet future demands breeding programs will most likely have to include additional traits, such as fitness related ones (survival, disease resistance), feed efficiency, or flesh quality, rather than only growth performance. In order to select for a multi-trait breeding objective, genetic variation in traits of interest and the genetic relationships among them need to be estimated. In addition, economic values for these traits will be required. Generally, there is a paucity of data on variable and fixed production costs in aquaculture, and this could be a major constraint in the further expansion of the breeding objectives. Secondly, genetic evaluation systems using the restricted maximum likelihood method (REML) and best linear unbiased prediction (BLUP) in a framework of mixed model methodology could be widely adopted to replace the more commonly used method of mass selection based on phenotypic performance. The BLUP method increases the accuracy of selection and also allows the management of inbreeding and estimation of genetic trends. BLUP is an improvement over the classic selection index approach, which was used in the success story of the genetically improved farmed tilapia (GIFT) in the Philippines, with genetic gains from 10 to 20 per cent per generation of selection. In parallel with BLUP, optimal genetic contribution theory can be applied to maximize genetic gain while constraining inbreeding in the long run in selection programs. Thirdly, by using advanced statistical methods, genetic selection can be carried out not only at the nucleus level but also in lower tiers of the pyramid breeding structure. Large scale across population genetic evaluation through genetic connectedness using cryopreserved sperm enables the comparison and ranking of genetic merit of all animals across populations, countries or years, and thus the genetically superior brood stock can be identified and widely used and exchanged to increase the rate of genetic progress in the population as a whole. It is concluded that sound genetic programs need to be established for aquaculture species. In addition to being very effective, fully pedigreed breeding programs would also enable the exploration of possibilities of integrating molecular markers (e.g., genetic tagging using DNA fingerprinting, marker (gene) assisted selection) and reproductive technologies such as in-vitro fertilization using cryopreserved spermatozoa.

Heat-shock protein70 gene expression in four hatchery Pacific Abalone Haliotis discus hannai Ino populations using for marker-assisted selection

Heat shock proteins (Hsps) are molecular chaperones that help organisms cope with stressful conditions. Here, we report on the growth rates and Hsp70 expressions in inbred and hybrid populations of abalone Haliotis discus hannai Ino. In abalone, inbred populations expressed more Hsp70 than hybrid populations at all temperatures, except at very high temperatures close to the physiological limit. At benign temperatures, there was a clear trend towards higher Hsp70 expression in inbred than hybrid populations, whereas at higher temperatures, a trend in the opposite direction was observed. The temperature of maximal Hsp70 expression (T-peak) varied with the population type. The T-peak of inbred populations (26 degrees C) was lower than that of the hybrid populations (28 degrees C). The maximal inducible Hsp70 of inbred populations was higher than that of hybrid populations. The results showed a trend towards higher expression in inbred population at a lower temperature. These results provide direct experimental evidence that hybrids can cope with the intrinsic stress even at non-stressful temperatures. The constitutive Hsp70 may therefore be used for marker-assisted selection in a breeding programme.

Molecular barley breeding

Breeding progress in barley yield in the UK is being sustained at a rate in the order of 1% per annum against a background of declining seed sales. Commercial barley breeders are largely concentrating upon the elite local gene pool but with genotypic evidence suggesting that there is still considerable variation between current recommended cultivars, even those produced as half-sibs by the same breeder. Marker Assisted Selection (MAS) protocols could be substituted for conventional selection for a number of major-gene targets but, in the majority of cases, conventional selection is more resource efficient. Results from current QTL mapping studies have not yet identified sufficiently robust and validated targets for UK barley breeders to adopt MAS to assist in the selection of complex traits such as yield and malting quality. Results from multiple population mapping amongst the elite gene pool being utilised by breeders and from association studies of elite germplasm tested as part of the UK recommended list trial process do, however, show some promise.

Validation of microsatellite markers for assisted selection of soybean genotypes resistant to powdery mildew

Powdery mildew is one of the most serious diseases of soybean and is found in all producing countries. The purpose of this study was to validate microsatellite markers previously identified as associated with resistance to powdery mildew in soybean. The study was conducted in two F, parent populations with contrasting resistance to powdery mildew, In the analysis 10 SSR primers were used for the populations. and tour polymorphic markers were identified for cross I (MGBR95-20937 x IAC-Foscarin 31) and three for cross 2 (MGBR-46 x Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) 48). The Chi-square analysis of the phenotypic evaluation confirmed the expected segregation (3: 1) of a dominant gene related to resistance. The polymorphic markers also segregated as expected (1:2:1). The markers Sat 366 and Sat 393 in the crosses 1 and 2. respectively, located at 9.41 and 12.45 cM from the gene. were considered promising for marker-assisted selection for resistance to powdery mildew in soybean. at a selection efficiency of 92.7% and 60.3% respectively.

A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore (Bos indicus) beef cattle

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

Analysis of key molecules of the innate immune system in mammary epithelial cells isolated from marker-assisted and conventionally selected cattle

Mastitis is the most prevalent infectious disease in dairy herds. Breeding programs considering mastitis susceptibility were adopted as approaches to improve udder health status. In recent decades, conventional selection criteria based on phenotypic characteristics such as somatic cell score in milk have been widely used to select animals. Recently, approaches to incorporate molecular information have become feasible because of the detection of quantitative trait loci (QTL) affecting mastitis resistance. The aims of the study were to explore molecular mechanisms underlying mastitis resistance and the genetic mechanisms underlying a QTL on Bos taurus chromosome 18 found to influence udder health. Primary cell cultures of mammary epithelial cells from heifers that were selected for high or low susceptibility to mastitis were established. Selection based on estimated pedigree breeding value or on the basis of marker-assisted selection using QTL information was implemented. The mRNA expression of 10 key molecules of the innate immune system was measured using quantitative real-time PCR after 1, 6, and 24 h of challenge with heat-inactivated mastitis pathogens (Escherichia coli and Staphylococcus aureus) and expression levels in the high and low susceptibility groups were compared according to selection criteria. In the marker-assisted selection groups, mRNA expression in cells isolated from less-susceptible animals was significantly elevated for toll-like receptor 2, tumor necrosis factor-alpha, IL-1beta, IL-6, IL-8, RANTES (regulated upon activation, normal t-cell expressed and secreted), complement factor C3, and lactoferrin. In the estimated pedigree breeding value groups, mRNA expression was significantly elevated only for V-rel reticuloendotheliosis viral oncogene homolog A, IL-1 beta, and RANTES. These observations provide first insights into genetically determined divergent reactions to pathogens in the bovine mammary gland and indicate that the application of QTL information could be a successful tool for the selection of animals resistant to mastitis.

Future trends in Animal Breeding due to new genetic tecnologies

The Darwin theory of evolution by natural selection is based on three principles: (a) variation; (b) inheritance; and (c) natural selection. Here, I take these principles as an excuse to review some topics related to the future research prospects in Animal Breeding. With respect to the first principle I describe two forms of variation different from mutation that are becoming increasingly important: variation in copy number and microRNAs. With respect to the second principle I comment on the possible relevance of non-mendelian inheritance, the so-called epigenetic effects, of which the genomic imprinting is the best characterized in domestic species. Regarding selection principle I emphasize the importance of selection for social traits and how this could contribute to both productivity and animal welfare. Finally, I analyse the impact of molecular biology in Animal Breeding, the achievements and limitations of quantitative trait locus and classical marker-assisted selection and the future of genomic selection

Molecular Breeding for Rainfed Lowland Rice in the Mekong Region

In the past 20 years, the rice-breeding program in Thailand had little success in developing new cultivars to replace Kao Dawk Mali 105 (KDML105) and Kao Khor 6 (RD6) for the tainted lowland rice environments. The main reason for the poor adoption of new cultivars by farmers is the susceptibility to diseases and unacceptable grain qualities. The conventional breeding program also takes at least 15 years from initial crossing to the release of new cultivars. A new breeding strategy can be established to shorten the period for cultivar improvement by using marker-assisted selection (MAS), rapid generations advance (RGA), and early generation testing in multi-locations for grain yield and qualities. Four generation of MAS backcross breeding were conducted to transfer genes and QTL for bacterial blight resistance (BLB), submergence tolerance (SUB), brown plant hopper resistance (BPH) and blast resistance (BL) into KDML105. Selected backcross lines, introgressed with target gene/QTL, were tolerant to SUB and resistant to BLB, BPH and BL. The agronomic performance and grain quality of these lines were as good as or better than KDML105.

Molecular breeding for rainfed lowland rice in the Mekong Region

In the past 20 years, the rice-breeding program in Thailand had little success in developing new cultivars to replace Kao Dawk Mali 105 (KDML105) and Kao Khor 6 (RD6). Main reason is a poor adoption of new cultivars by farmers due to poor adaptation of new cultivars to the rainfed environments, susceptibility to diseases and insect pests and unacceptable grain qualities. The conventional breeding program also takes at least 15 years for releasing new cultivars. New breeding strategy can be established to shorten period for cultivar improvement by using marker-assisted selection (MAS), rapid generations advance (RGA), early generation testing in multi-locations for grain yield and qualities. Four generation of MAS backcross breeding were conducted to transfer gene and QTL for bacterial blight resistance (BLB), submergence tolerance (SUB), brown planthopper resistance (BPH) and blast resistance (BL) into KDML105. Selected backcross lines, introgressed with target gene/QTL, were tolerant to SUB and resistant to BLB, BPH and BL. The agronomic performance and grain quality of these lines were as good as or better than KDML105.