F3 Families Research Articles

Statistical dissection of cyto-nuclear epistasis subject to genomic imprinting in line crosses.

Cytoplasm contains important metabolism reaction organelles such as mitochondria and chloroplast (in plant). In particular, mitochondria contains special DNA information which can be passed to offsprings through maternal gametes, and has been confirmed to play a pivotal role in nuclear activities. Experimental evidences have documented the importance of cyto-nuclear interactions in affecting important biological traits. While studies have also pointed out the role of interaction between imprinting nuclear DNA and cytoplasm, no statistical method has been developed to efficiently model such effect and further quantify its effect size. In this work, we developed an efficient statistical model for genome-wide estimating and testing the cytoplasmic effect, nuclear DNA imprinting effect as well as the interaction between them under reciprocal backcross and F2 designs derived from inbred lines. Parameters are estimated under maximum likelihood framework implemented with the EM algorithm. Extensive simulations show good performance in a variety of scenarios. The utility of the method is demonstrated by analyzing a published data set in an F2 family derived from C3H/HeJBir and C57BL/6 J mouse strains. Important cyto-nuclear interactions were identified. Our approach provides a quantitative framework for identifying and estimating cyto-nuclear interactions subject to genomic imprinting involved in the genetic control of complex traits.

A Genome Scan for Quantitative Trait Loci Associated with Vibrio anguillarum Infection Resistance in Japanese Flounder (Paralichthys olivaceus) by Bulked Segregant Analysis

A recent genetic linkage map was employed to detect quantitative trait loci (QTLs) associated with Vibrio anguillarum resistance in Japanese flounder. An F1 family established and challenged with V. anguillarum in 2009 was used for QTL mapping. Of the 221 simple sequence repeat (SSR) markers used to detect polymorphisms in the parents of F1, 170 were confirmed to be polymorphic. The average distance between the markers was 10.6 cM. Equal amounts of genomic DNA from 15 fry that died early and from 15 survivors were pooled separately to constitute susceptible bulk and resistance bulk DNA. Bulked segregant analysis and QTL mapping were combined to detect candidate SSR markers and regions associated with the disease. A genome scan identified four polymorphic SSR markers, two of which were significantly different between susceptible and resistance bulk (P=0.008). These two markers were located in linkage group (LG) 7; therefore, all the SSR markers in LG7 were genotyped in all the challenged fry by single marker analysis. Using two different models, 11-17 SSR markers were detected with different levels of significance. To confirm the associations of these markers with the disease, composite interval mapping was employed to genotype all the challenged individuals. One and three QTLs, which explained more than 60 % of the phenotypic variance, were detected by the two models. Two of the QTLs were located at 48.6 cM. The common QTL may therefore be a major candidate region for disease resistance against V. anguillarum infection.

Genetic Studies on Some Earliness and Agronomic Characters in Advanced Generations in Bread Wheat (Triticum aestivum L.)

The early generation (F3 families) analysis measured the variance components of three crosses of five diverse parents. This work carried during three years 2010-13 at the experimental farm of Sakha Agricultural Research Station, Kafr El-Sheikh governorate, Egypt. The Data were recorded on days to heading, days to maturity, grain filling period and rate, plant height, number of spikes per plant, number of kernels per spike, 100kernel weight and grain yield. The F3 families had highly significant differences in most cases. The ranges of the performance of the F3 families exceeded the limits of the minus and plus directions of their parents for most characters, showing the ability of selection for the desirable directions for these characters. The magnitude of genetic variance among the F3 families exceeded corresponding environmental variance, while the environmental variance was higher than or almost equal to the corresponding genetic variance among plants within families for most characters. The additive and dominance variances were important in all cases. The broad and narrow sense heritability and genetic advance estimates were relatively medium to high for most characters. 5% of plants for each cross were selected for ealry mature and high yielding to evaluate in sperate experment in the next season. Conference Proceeding Full Paper Aglan and Farhat; IJPSS, Article no. IJPSS.2014.6.020 791

Lr67/Yr46 confers adult plant resistance to stem rust and powdery mildew in wheat

We demonstrate that Lr67/Yr46 has pleiotropic effect on stem rust and powdery mildew resistance and is associated with leaf tip necrosis. Genes are designated as Sr55, Pm46 and Ltn3 , respectively. Wheat (Triticum aestivum) accession RL6077, known to carry the pleiotropic slow rusting leaf and yellow rust resistance genes Lr67/Yr46 in Thatcher background, displayed significantly lower stem rust (P. graminis tritici; Pgt) and powdery mildew (Blumeria graminis tritici; Bgt) severities in Kenya and in Norway, respectively, compared to its recurrent parent Thatcher. We investigated the resistance of RL6077 to stem rust and powdery mildew using Avocet × RL6077 F6 recombinant inbred lines (RILs) derived from two photoperiod-insensitive F3 families segregating for Lr67/Yr46. Greenhouse seedling tests were conducted with Mexican Pgt race RTR. Field evaluations were conducted under artificially initiated stem rust epidemics with Pgt races RTR and TTKST (Ug99 + Sr24) at Ciudad Obregon (Mexico) and Njoro (Kenya) during 2010-2011; and under natural powdery mildew epiphytotic in Norway at Ås and Hamar during 2011 and 2012. In Mexico, a mean reduction of 41 % on stem rust severity was obtained for RILs carrying Lr67/Yr46, compared to RILs that lacked the gene, whereas in Kenya the difference was smaller (16 %) but significant. In Norway, leaf tip necrosis was associated with Lr67/Yr46 and RILs carrying Lr67/Yr46 showed a 20 % reduction in mean powdery mildew severity at both sites across the 2 years of evaluation. Our study demonstrates that Lr67/Yr46 confers partial resistance to stem rust and powdery mildew and is associated with leaf tip necrosis. The corresponding pleiotropic, or tightly linked, genes, designated as Sr55, Pm46, and Ltn3, can be utilized to provide broad-spectrum durable disease resistance in wheat.

Major QTLs Control Resistance to Rice Hoja Blanca Virus and Its VectorTagosodes orizicolus

Rice hoja blanca (white leaf) disease can cause severe yield losses in rice in the Americas. The disease is caused by the rice hoja blanca virus (RHBV), which is transmitted by the planthopper vector Tagosodes orizicolus. Because classical breeding schemes for this disease rely on expensive, time-consuming screenings, there is a need for alternatives such as marker-aided selection. The varieties Fedearroz 2000 and Fedearroz 50, which are resistant to RHBV and to the feeding damage caused by T. orizicolus, were crossed with the susceptible line WC366 to produce segregating F2:3 populations. The F3 families were scored for their resistance level to RHBV and T. orizicolus. The F2:3 lines of both crosses were genotyped using microsatellite markers. One major QTL on the short arm of chromosome 4 was identified for resistance to RHBV in the two populations. Two major QTL on chromosomes 5 and 7 were identified for resistance to T. orizicolus in the Fd2000 × WC366 and Fd50 × WC366 crosses, respectively. This comparative study using two distinct rice populations allowed for a better understanding of how the resistance to RHBV and its vector are controlled genetically. Simple marker-aided breeding schemes based on QTL information can be designed to improve rice germplasm to reduce losses caused by this important disease.

Molecular approaches for wheat improvement under drought and heat stress

Novel molecular breeding selection strategies were implemented in breeding programs in India for wheat improvement under drought and heat stress. Elite Indian varieties HD2733 and GW322 were targeted for improvement to abiotic stresses through marker assisted backcross breeding approach. Backcross populations were advanced to BC1/BC2 F2 after tracking QTLs for foreground selection covering traits such as canopy temperature (CT), chlorophyll content, normalized difference vegetation index (NDVI), grain filling duration (GFD), thousand kernel weight, grain yield and a range of polymorphic microsatellite markers covering entire genome (4–5 SSR markers per chromosome) being used for tracking the recurrent parent genome. Marker assisted recurrent selection (MARS) involved estimation of marker effects for several small effect/major QTLs followed by two recombination cycles. Designed intermating among selected F5 families were carried out after conducting ANOVA and AMMI analysis on multi-location yield trials and polymorphic markers among the parents in two biparental base populations (F5). Inter-family intermating among the best identified families carried out in different combinations to accumulate and recombine 4–8 QTLs per intermated progeny and confirmed in selfed homozygous lines.

Genetic linkage map and QTL analysis of partial resistance to black stem in sunflower (Helianthus annuus L.)

Black stem, caused by Phoma macdonaldii, is one of the most important diseases of sunflower in the world. Quantitative trait loci (QTLs) implicated in partial resistance to three isolates of P. macdonaldii including MA6, MP6 and MP10 were investigated using F2/F3 population from the cross between sunflower resistant mutant line ‘M6-54-1’ and susceptible inbred line ‘ENSAT-B4’. A genetic linkage map was constructed with 88 amplified fragment length polymorphism (AFLP) and 44 simple sequence repeat (SSR) markers using 101 F2 individuals. The map comprises 17 linkage groups (LGs) with an overall length of 1,490 cM and mean density of one marker per 12.44 cM. Parental lines and their 101 F3 families were evaluated for their resistance to P. macdonalii isolates in controlled conditions in a randomized complete block design with three replications. High genetic variability and transgressive segregation were observed among F3 families for partial resistance to all of three P. macdonaldii isolates. Composite interval mapping analysis revealed 14 putative QTLs, localized on seven linkage groups, with phenotypic variance ranging from 4 to 42 %. The QTL bsrMP6.8.1 was detected as non isolate-specific QTL and the rest of them were ‘isolate-specific’ QTLs. The major QTL on LG8 which was involved in partial resistance to three isolates could be good candidate to introduce resistance to three P. macdonaldii isolates into elite sunflower breeding lines via marker assisted breeding program.

Comparative analysis of disease resistance among three successive generations of Japanese flounder (<I>Paralichthys olivaceus</I>) fam-ilies

Japanese flounder(Paralichthys olivaceus) is a widely cultured marine fish species in China and is highly valued because of its fast growth and good flavor. However, frequent occurrence of disease and subsequent losses limit profitability and aquaculture development. Breeding a new flounder strain with enhanced disease resistance is an important task in marine fish aquaculture. In the present study, new Japanese flounder families were established based on Japanese stock(JS), Korean stock(KS), and stock with high resistance to Vibrio anguillarum(RS) by nested hybrid, cross, and gynogenesis. Forty-three and sixty-five Japanese flounder families were established in 2009 and 2012, respectively. Disease resistance was investigated using 33 families in 2009 and 43 in2012 through intraperitoneal injection challenged with V. anguillarum. The results demonstrate that different families exhibited variable survival rates and 13 families with high disease resistance were obtained. All 13 families exhibited significantly higher survival rates compared with the control, however, some were more significant than others(P0.01 in 3 families; P0.05 in 10 families). Of these 13 families, three were derived from the F2family, one from the F3 family, and two belonged to the first and second gynogenesis generations(G1 and G2). In these six families, disease resistance was high in the parents, with the exception of the F2 family; their survival rate variation coefficients were 10%. Analysis of disease resistance in the three successive generations revealed that, 13 of the 16 disease-resistance families which included 13 families mentioned above and 3 resistant families sereened in 2007 were derived from RS. In conclusion, some F2, F3, G1, and G2 families exhibited enhanced disease resistance inherited from their parents, indicating that the establishment of a disease-resistant strain based on these families is possible.

Interrelationship and path coefficient analysis of yield components in F4 progenies of tef (Eragrostis tef).

This experiment was conducted at Debre Zeit and Akaki during 2004-2005 cropping season on F2-derived F4 bulk families of three crosses, viz, DZ-01-974 x DZ-01-2786, DZ-01-974 x DZ-Cr-37 and Alba x Kaye Murri. To estimate the correlations and path coefficients between yield and yield components, 63 F4 families were taken randomly from each of the three crosses. The 189 F4 families, five parents and two checks were space planted following in 14 x 14 simple lattice design. Study of associations among traits indicated that yield was positively associated with shoot biomass, harvest index, lodging index and panicle kernel weight at phenotypic level at Debre Zeit. At Akaki, yield had significant positive correlation with shoot biomass, harvest index, plant height, panicle length and panicle weight. At genotypic level, grain yield per plot exhibited positive association with harvest index, shoot biomass, lodging index and panicle kernel weight at Debre Zeit. By contrast, days to heading, days to maturity, plant height and panicle length showed negative association with yield. At Akaki, kernel yield per plot was positively correlated at genotypic level with all the traits considered where lodging index had the highest correlation followed by shoot biomass, panicle kernel weight and harvest index. Path coefficient analysis at both phenotypic and genotypic levels for both the locations suggested those shoot biomass and harvest indexes are the two important yield determining traits. These two traits might be useful in indirect selection for yield improvement in the material generated from the three crosses under consideration.

A frameshift mutation in the melanophilin gene causes the dilute coat colour in rabbit (Oryctolagus cuniculus) breeds

In rabbit, the dilute locus is determined by a recessive mutated allele (d) that causes the dilution of both eumelanic and pheomelanic pigmentations. In mice, similar phenotypes are determined by mutations in the myosin VA, Rab27a and melanophilin (MLPH) genes. In this study, we investigated the rabbit MLPH gene and showed that a mutation in this gene appears responsible for the dilute coat colour in this species. Checkered Giant F1 families segregating for black and grey (diluted or blue) coat colour were first genotyped for a complex indel in intron 1 of the MLPH gene that was completely associated with the coat colour phenotype (θ = 0.00; LOD = 4.82). Then, we sequenced 6357 bp of the MLPH gene in 18 rabbits of different coat colours, including blue animals. A total of 165 polymorphisms were identified: 137 were in non-coding regions and 28 were in coding exons. One of them was a frameshift deletion in exon 5. Genotyping the half-sib families confirmed the complete cosegregation of this mutation with the blue coat colour. The mutation was analysed in 198 rabbits of 23 breeds. All Blue Vienna and all other blue/grey/ash rabbits in other breeds (Californian, Castor Rex, Checkered Giant, English Spot, Fairy Marburg and Fairy Pearly) were homozygous for this deletion. The identification of MLPH as the responsible gene for the dilute locus in rabbit provides a natural animal model for human Griscelli syndrome type 3 and a new mutant to study the role of this gene on pigmentation.

Characterizations of Shell and Mantle Edge Pigmentation of a Pacific Oyster, Crassostrea gigas, in Korean Peninsula.

The objectives of this study were to investigate color patterns of shell and mantle edge pigmentation of a Pacific oyster, C. gigas, and to estimate variance components of the two colors. A sample of 240 F0 oysters was collected from six aquaculture farms in Tongyeong, Korea to measure shell color and mantle edge pigmentation. Among the F0s, male and female individuals with black (white) shell and black (white) mantle edge were selected and mated to generate three F1 full-sib black (white) cross families (N = 265). Two and four F2 cross families (N = 286) were also produced from black and white F1 selected individuals, respectively. Variance component estimates due to residuals and families within color were obtained using SAS PROC VARCOMP procedures to estimate heritability of shell and mantle edge pigmentation. In the F0 generation, about 29% (11%) had black (white) color for both shell and mantle edge. However, in the F1 and F2 black (white) cross families, 75% (67%) and 100% (100%) of oysters had black (white) shell colors, and 59% (23%) and 79% (55%) had black (white) mantle edge, respectively. Spearman correlation coefficients between shell and mantle edge color were 0.25, 0.74, and 0.92 in F0, F1, and F2 generations, respectively, indicating that, with generations of selection process, an individual with black (white) shell color is more likely to have black (white) mantle edge pigmentation. This suggests that shell color could be a good indicator trait for mantle edge pigmentation if selection of both the colors is implemented for a couple of generations. Estimates of heritability were 0.41 and 0.77 for shell color and 0.27 and 0.08 for mantle edge pigmentation in the F1 and F2 generations, respectively, indicating that, in general, significant proportions of phenotypic variations for the shell and mantle edge colors are explained by genetic variations between individuals. These results suggest that the two color traits are inheritable and correlated, enabling effective selection on shell and mantle edge color.

Mechanism of Resistance and Inheritance in Glyphosate Resistant Palmer amaranth (Amaranthus palmeri) Populations from New Mexico, USA

Two populations of Palmer amaranth from New Mexico have been confirmed to be resistant to glyphosate. In the present study, the molecular basis of resistance and the mode of inheritance of resistance in those populations were investigated. Quantitative real-time polymerase chain reaction analysis indicated up to an eightfold increase in genomicEPSPScopy number in glyphosate resistant plants compared with susceptible plants. The relative genomicEPSPScopy number of resistant plants was positively correlated with the relativeEPSPScDNA expression levels. Eight hours after treatment with glyphosate, the shikimate accumulation levels in resistant plants were negatively correlated with the genomicEPSPScopy numbers. Multiple sequencing of theEPSPScDNA of resistant plants did not reveal any glyphosate resistance-conferring mutations. The evaluation of F1, reciprocal F1, and F2Palmer amaranth families indicated that resistance to glyphosate does not follow a single-gene segregation pattern. Results suggest that theEPSPSamplification is the primary molecular basis of resistance in glyphosate resistant populations of Palmer amaranth from New Mexico.

Genetic analyses of bolting in bulb onion (Allium cepa L.)

We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. 'Bolting', or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima's D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large 'Nasik Red × CUDH2150' F2 family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F2 families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.

Mapping Quantitative Trait Loci for Powdery Mildew Resistance in Flax (Linum usitatissimum L.)

ABSTRACTPowdery mildew (Oidium lini Skoric, [PM]), an obligate biotrophic ascomycete, is a common and widespread foliar disease of flax in most flax‐growing areas of the world. In this study, we constructed a linkage map using 143 simple sequence repeat (SSR) markers and an F2 population of 300 individuals generated from a cross between the susceptible cultivar NorMan and the resistant cultivar Linda. The F2–derived F3 families were phenotyped in the field and the F3–derived F4 families were phenotyped in a controlled environment growth chamber. The 15 linkage group map covered 1241 cM and was largely collinear with the previously published consensus map. Quantitative trait loci (QTL) analysis was performed and three PM resistance QTL located on LG1, 7, and 9 were identified consistently using phenotyping data from both field and growth chamber studies. These QTL explained 97% of the phenotypic variation exhibiting a mainly dominant gene action. This work represents a first step toward understanding the genetics of PM resistance in flax and map‐based cloning of candidate genes underlying the QTL.

Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet

Linkage analysis confirmed the association in the region of PHYC in pearl millet. The comparison of genes found in this region suggests that PHYC is the best candidate. Major efforts are currently underway to dissect the phenotype-genotype relationship in plants and animals using existing populations. This method exploits historical recombinations accumulated in these populations. However, linkage disequilibrium sometimes extends over a relatively long distance, particularly in genomic regions containing polymorphisms that have been targets for selection. In this case, many genes in the region could be statistically associated with the trait shaped by the selected polymorphism. Statistical analyses could help in identifying the best candidate genes into such a region where an association is found. In a previous study, we proposed that a fragment of the PHYTOCHROME C gene (PHYC) is associated with flowering time and morphological variations in pearl millet. In the present study, we first performed linkage analyses using three pearl millet F2 families to confirm the presence of a QTL in the vicinity of PHYC. We then analyzed a wider genomic region of~100kb around PHYC to pinpoint the gene that best explains the association with the trait in this region. A panel of 90 pearl millet inbred lines was used to assess the association. We used a Markov chain Monte Carlo approach to compare 75 markers distributed along this 100-kb region. We found the best candidate markers on the PHYC gene. Signatures of selection in this region were assessed in an independent data set and pointed to the same gene. These results foster confidence in the likely role of PHYC in phenotypic variation and encourage the development of functional studies.

Cytoplasmic Male Sterility Contributes to Hybrid Incompatibility Between Subspecies ofArabidopsis lyrata

In crosses between evolutionarily diverged populations, genomic incompatibilities may result in sterile hybrids, indicating evolution of reproductive isolation. In several plant families, crosses within a population can also lead to male sterile progeny because of conflict between the maternally and biparentally inherited genomes. We examined hybrid fertility between subspecies of the perennial outcrossing self-incompatible Lyrate rockcress (Arabidopsis lyrata) in large reciprocal F2 progenies and three generations of backcrosses. In one of the reciprocal F2 progenies, almost one-fourth of the plants were male-sterile. Correspondingly, almost one-half of the plants in one of the four reciprocal backcross progenies expressed male sterility. In an additional four independent F2 and backcross families, three segregated male sterility. The observed asymmetrical hybrid incompatibility is attributable to male sterility factors in one cytoplasm, for which the other population lacks effective fertility restorers. Genotyping of 96 molecular markers and quantitative trait locus mapping revealed that only 60% of the plants having the male sterile cytoplasm and lacking the corresponding restorers were phenotypically male-sterile. Genotyping data showed that there is only one restorer locus, which mapped to a 600-kb interval at the top of chromosome 2 in a region containing a cluster of pentatricopeptide repeat genes. Male fertility showed no trade-off with seed production. We discuss the role of cytoplasm and genomic conflict in incipient speciation and conclude that cytoplasmic male sterility–lowering hybrid fitness is a transient effect with limited potential to form permanent reproductive barriers between diverged populations of hermaphrodite self-incompatible species.

Development of the gene-based SCARs for the Ph-3 locus, which confers late blight resistance in tomato

Late blight (LB) is a devastating disease in tomato (Solanum lycopersicum), which is caused by the oomycete Phytophthora infestans (Mont.) de Bary. In this study, the LB-resistance gene Ph-3 was evaluated using a pathogenic isolate of P. infestans from Korea. Molecular mapping of the TG328 and TG591 regions, which are tightly linked to the Ph-3 locus, was performed using F6 families derived by crossing the LB-resistant accession “L3708” (Solanum pimpinellifolium) with the LB-susceptible accession “AV107-4” (S. lycopersicum). The map indicated that the Ph-3 locus also conferred high resistance to the Korean isolate of P. infestans. To identify the putative Ph-3 gene, the ultracontig SL2.4ch09 of the S. pimpinellifolium draft-genome sequence, which contained the TG328 and TG591 clone sequences, was investigated. Four tandemly duplicated putative Ph-3 homologs (designated as Ph-3a, Ph-3b, Ph-3c, and Ph-3d in this study) belonging to the coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) class of pathogen resistance genes were identified in a flanking region of TG328 and TG591. TG591 sequences and partial sequences of Ph-3c and Ph-3d were tandemly repeated. Protein sequences of Ph-3 homologs showed high sequence homology with Rpi-vnt1.1 and Rpi-vnt1.3, the CC-NBS-LRR LB-resistance genes in potato. Ph-3c and Ph-3d showed the highest protein sequence homology (80%) to Rpi-vnt1.1 and Rpi-vnt1.3, whereas Ph-3a and Ph-3b showed 70% homology to these genes. A set of sequence characterized amplified region (SCAR) markers that could distinguish each copy of the Ph-3 gene homolog were developed, and allelic compositions of the Ph-3 locus were compared between “L3708” and a variety of LB-susceptible tomato accessions. These SCAR markers proved useful, not only for studying the organization of the Ph-3 homologs in an individual tomato plant, but also for selection of the LB-resistance allele.

Response to farmer mass selection in early generation progeny of bread wheat landrace crosses

AbstractA participatory plant breeding (PPB) program involving the French farmers' association ‘Réseau Semences Paysannes’ and the French National Agricultural Research Institute (INRA) at Le Moulon was initiated in 2005. In the process of designing the breeding scheme, we evaluated the impact of farmer selection at an early stage (F2) on bread wheat cross progeny populations. The objectives were to characterize the effect of farmer selection, to evaluate the impact of farmer selection on intra-varietal diversity, to provide farmers with relevant information that they can use to improve their selection practices. Early selection was found efficient for some traits and for some of the 35 F2-derived F3 families. For traits of interest such as thousand kernel weight or grain weight per spike, when the response was significant, it was always positive. For most of the traits studied, the among-family genetic variance increased after selection while the average within-family genetic variance decreased. This study provides the first quantitative results for this PPB program and information that will help optimize it in the future.

Mapping Quantitative Trait Loci for Omega-3 Fatty Acids in Asian Seabass

Omega-3 fatty acids are essential fatty acids for human health. Therefore, increasing both percentage of omega-3 and a better fatty acid profile in fish fillets is one of the breeding goals in aquaculture. However, it is difficult to increase the omega-3 content in fish fillets, as the phenotypic selection of these traits is not easily feasible. To facilitate the genetic improvement of the Asian seabass for optimal fatty acid profiles, a genome-wide scan for quantitative trait loci (QTL) affecting fatty acid level in the flesh of the Asian seabass was performed on an F2 family containing 314 offspring. All family members were genotyped using 123 informative microsatellites and 22 SNPs. High percentages of n-3 polyunsaturated fatty acids (PUFA), especially C22:6 (DHA 16.48 ± 3.09%) and C20:5 (EPA 7.19 ± 0.86%) were detected in the flesh. One significant and 54 suggestive QTL for different fatty acids and a water content trait were detected on the whole genome. QTL for C18:0b was located on linkage groups (LG) 5. QTL for total n-3 PUFA content in flesh were mapped onto LG6 and LG23 with the phenotypic variance explained ranging from 3.8 to 6.3%. Four QTL for C22:6 were detected on LG6, LG23, and LG24, explaining 3.9 to 4.9% of the phenotypic variance, respectively. Mapping of QTL for contents of different fatty acids is the first step towards improving the omega-3 content in the fillets of fish by using marker-assisted selection and is important for understanding the biology of fatty acid deposition.

Identification of quantitative trait loci for growth-related traits in the swimming crabPortunus trituberculatus

The swimming crab (Portunus trituberculatus) is an economically important species in Asian aquaculture. Implementing growth-related traits of P. trituberculatus into genetic breeding programmes is an ongoing effort. We used a previously published genetic linkage map of P. trituberculatus, containing 55 simple sequence repeat (SSR) markers and 172 amplified fragment length polymorphism (AFLP) techniques to map quantitative trait loci (QTL) for growth-related traits in a single full sibling F2 family. Ten growth-related traits were measured for QTL mapping. Composite interval mapping identified 9 QTL on the female map and 16 on the male map. Individual QTL with additive effects explained 11–38% of the phenotypic variance for various traits using the female parent's map, and from 1% to 21% using the male parent's map. Two QTL explaining a large percentage of variation in body weight were detected on chromosome 17 on the female map, and on chromosome 16 on the male map, and contributed 38% and 18% of the phenotypic variance respectively. This is the first study to report the detection and positioning of major QTL affecting growth in a true crab species (Brachyura). The mapping of growth-related QTL in this study raises the possibility of improving the growth of P. trituberculatus through marker-assisted selection.