The seed size and shape of lentil are important traits because they determine the market class, cooking time, and can influence quality and yield of milled lentils. Understanding the genetic control of seed size and shape can help breeders develop varieties with improved seed size and shape characteristics such as seed diameter, seed thickness and seed plumpness. The objectives were to determine the heritability of seed size and shape and identify the genomic regions controlling these traits. This involved i) developing a linkage map for the LR-18 population (CDC Robin x 964a-46) using a recently developed single nucleotide polymorphism (SNP) assay; ii) analyzing the LR-18 population for seed size and shape QTLs; iii) analyzing an association mapping panel for seed size and shape QTLs. Phenotyping trials were grown at two different locations in Saskatchewan, Canada. The mapping population was grown in two different years while the association panel was only grown in one. Seed diameter and thickness were measured using sieves and this data were used to calculate seed plumpness. Days to flowering was also recorded to determine if it had any effect on seed size or shape. A linkage map consisting of 537 SNPs, 10 SSRs and 4 morphological markers on seven linkage groups was constructed and used for the QTL analysis. The heritability estimates were high for seed diameter and seed plumpness (0.92 and 0.94, respectively) while for seed thickness and days to flowering they were more moderate (0.60 and 0.45, respectively). QTL analysis revealed QTLs on five of the seven linkage groups. The association mapping study revealed similar heritability estimates of 0.97, 0.62, 0.94, and 0.62 for seed diameter, seed thickness, seed plumpness and flowering time, respectively. There were 31 different significant marker trait associations, however only 5 of those were significant for both locations. Four of those five markers did not map in the LR-18 linkage map so their genomic locations are still to be determined. Results showed that there are key regions in the genome that control seed size and shape and flowering time in lentil. These markers could be used for marker-assisted selection or for further candidate gene analysis.

[Abstract]Quantitative Trait Loci (QTLs) for polyphenol oxidase and xanthophyll have a significant impact on variation in wheat flour for noodle colour and colour stability. QTLs from two Australian wheat cultivars, Sunco and Tasman, have been backcrossed into two Chinese wheat varieties, Chuanmai 22 and Mianyang 11, to assess marker predictability for these important traits in significantly different genetic backgrounds. The concept of Marker-Assisted-Selection (MAS) is being trialled in this study as a proposed method for wheat improvement. In this approach molecular markers are used in conjunction with backcross breeding methods to introgress specific characters into elite breeding materials, with the goal of improving the quality attributes of wheat for the Asian noodle market. After three single seed descent generations, the backcross populations generated allow four QTLs to be investigated. These include two for polyphenol oxidase (chromosome 2A and 2D) and two for xanthophyll (chromosome 3B and 7A). This research was successful in identifying microsatellite markers that are capable of predicting PPO activity levels and Xanthophyll content within the backcross populations. These microsatellites were validated as useful markers for these quality traits, as they have also found to be important in the Sunco x Tasman doubled haploid population. The combination of marker assisted selection and backcrossing has generated three lines that contain different combinations of the PPO activity and Xanthophyll content QTLs. These lines have been found to produce low levels of PPO activity and have a low Xanthophyll content. This improvement in flour colour and colour stability highlights the potential of marker assisted selection as a useful tool in wheat breeding.

Phytophthora sojae, the causal organism of stem and root rot, and <i>Soybean mosaic virus</i> (SMV) cause two of the most highly destructive diseases of soybean (<i>Glycine max</i> L. Merr). <i>P. sojae</i> can be managed either through deployment of race-specific resistance or through quantitative resistance termed partial resistance. In the current study, partial resistance to <i>P. sojae</i> was mapped in an interspecific recombinant inbred line (RIL) population of <i>Glycine max</i> by <i>Glycine soja</i>. One major quantitative trait loci (QTL) on molecular linkage group (MLG)-J (chromosome 16) and two minor QTL on MLG-I (chromosome 20) and -G (chromosome 18) were mapped using conventional molecular markers. Additionally, partial resistance to <i>P. sojae</i> was mapped in the same RIL population using single feature polymorphism (SFP) markers that further fine mapped the <i>P. sojae</i> QTL and identified potential candidate genes contributing to resistance. In a separate study, race-specific resistance was characterized in PI96983 discovering a potentially new allele of <i>Rps4</i> on MLG-G. Finally, using the newly available whole-genome shotgun sequence of soybean, <i>Rsv4</i> conferring resistance to strains of SMV known in the US, was localized to an approximately 100 kb region of sequence on chromosome 2 (MLG-D1B). Newly designed PCR-based markers permit for efficient selection of <i>Rsv4</i> by breeding programs. Identified candidate genes for <i>Rsv4</i> are discussed. Genomic resources developed in all of these studies provide breeders the tools necessary for developing durable resistance to both SMV and <i>P. sojae</i>. / Ph. D.

Citrus is the main fruit crop in the world and Spain is the 6th producer and the major exporter for the fresh fruit market. Seedlessness is one of the most important fruit quality traits for this market since consumers do not accept seedy fruits. Recovery of triploid hybrids has become an important breeding strategy to develop new seedless citrus varieties and several of them have been already released from citrus breeding programs worldwide. Despite the undisputable importance of polyploidy in plant species, their genetics are much less well known than those of their diploid counterparts. Citrus triploid hybrids can be routinely recovered from sexual polyploidization (2x ¿ 2x) or interploid crosses (2x ¿ 4x and 4x ¿ 2x). In 2x ¿ 2x sexual crosses, spontaneous triploid hybrids arise from the union of an unreduced (2n) megagametophyte with haploid pollen. In the case of interploid sexual crosses (2x ¿ 4x and 4x ¿ 2x), triploid hybrids result from the fecundation of a diploid gamete arising from the tetraploid parent and a haploid gamete arising from the diploid parent. The genetic and phenotypic structures of triploid populations greatly depend on the parental heterozygosity restitution (HR) in the diploid gamete at each locus, which is mainly affected by the triploid recovery strategy. In 2x ¿ 2x crosses, HR depends on the underlying mechanism leading to the unreduced gamete formation, which are genetically equivalent to First Division Restitution (FDR) or Second Division Restitution (SDR) mechanisms. Moreover, under each restitution mechanism, HR also depends on the locus-centromere genetic distance. In the case of interploid crosses, parental heterozygosity restitution from tetraploid parents depends on the double reduction frequency. In citrus, the unreduced gamete formation mechanism is still controversial; FDR has been the mechanism proposed for sweet orange, whereas SDR has been proposed for clementine. On the other hand, inferring the allelic configurations of genetic markers is a main challenge in polyploidy crops to infer genotypic and gametic structures with the objective to analyze meiosis and inheritance mechanisms. According to this scientific context, the objectives of the thesis where: (i) to develop a new approach for allele dosis assignation when using co-dominant markers, (ii) to implement and apply methods for the analysis of 2n gametes origin and locate centromeres, and (iii) to take advantage of this knowledge to locate a major gene of resistance to Alternaria Brown Spot (ABS) which is a major constraint for triploid mandarin breeding. For microsatellite (SSR) markers, we have demonstrated that triploid progeny genotyping can be successfully performed using the microsatellite allele-counting peak ratio (MAC-PR) method. However, SSR analysis remains relatively costly and time consuming compared with actual SNP genotyping methods. Moreover, with the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers that can be selected along the entire genome. In this thesis, a new method based on competitive allele-specific PCR has been developed to assign SNP allele dosage in an accurate, simple, and cost effective way. Combining the MAC-PR and the new developed SNP genotyping methods offers the possibility to utilize a broad range of molecular markers in genotyping triploid genotypes. Both methods have been used in further works included in this thesis. SDR has been demonstrated as the mechanism underlying unreduced gamete production in `Fortune¿ mandarin by genotyping triploid progenies with SSR markers. In addition, a new method to locate the centromere, based on the best fit between observed heterozygosity restitution within a linkage group and theoretical functions under either partial or no chiasma interference hypotheses has been developed and successfully applied. To expand the knowledge of the mechanism underlying unreduced gamete formation to other citrus genotypes besides clementines and `Fortune¿ mandarin, a maximum likelihood method based on parental heterozygosity restitution of centromeric loci was developed and successfully applied in sixteen mandarin cultivars. The new method developed in the study allows inferring the restitution mechanism both at population level and even at individual level. Maternal origin of 2n gametes was confirmed for all triploid hybrids and SDR was proposed as the restitution mechanism for all analyzed progenies. The information acquired from the mode of heterozygosity restitution in citrus was useful to determine the genetic and phenotypic structures of new triploid populations arising from different breeding strategies. We studied these structures for the resistance to Alternaria brown spot (ABS), a serious fungal disease producing necrotic lesions on fruits and young leaves in susceptible citrus genotypes. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from SDR to map a genome region linked to ABS resistance in triploid citrus progeny. The monolocus dominant inheritance of the susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. A 3.3 Mb genomic region linked to ABS resistance was located near the centromere on chromosome III, which includes clusters of resistance genes. SSR and SNP markers were developed for an efficient early selection of ABS resistant hybrids and they are currently used in our breeding program to perform marker assisted selection. The knowledge obtained in this thesis on the mechanism of sexual polyploidization and inheritance of concrete traits in citrus will allow implementing much more efficient triploid breeding programs on the basis of current and future needs. Indeed, applied outcomes of this PhD are already routinely used in the IVIA triploid breeding program. / Cuenca Ibáñez, J. (2013). Mechanisms of sexual polyploidization and inheritance in triploid citrus populations [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/34671 / TESIS / Premios Extraordinarios de tesis doctorales

No description available.

Fusarium head blight (FHB) is one of the most destructive diseases of common wheat (Triticum eastivum L.) worldwide. Resistance to FHB is an ideal trait for which molecular marker assisted selection (MAS) would facilitate breeding and cultivar development efforts. Validation of quantitative trait loci (QTL) conferring FHB resistance is a prerequisite for MAS. This study was conducted to validate and evaluate the effect of two major QTL, previously reported on chromosomes 3BS and 5AS, on multiple FHB resistance components in two independent studies, one involving a mapping population derived from a cross between a known resistance source W14 and a susceptible soft red winter (SRW) wheat cultivar Pioneer2684, and the other involving seventy adapted SRW wheat lines. The first study confirmed that the 3BS and 5AS QTL were significantly associated with FHB resistance and further indicated that the 3BS QTL has a larger effect on three FHB resistance components (type II and III resistance and resistance to Fusarium Damaged kernels) evaluated in greenhouse experiments, while the 5AS QTL has a larger effect on type I resistance evaluated in a field experiment. Six simple sequence repeat (SSR) and two sequence targeted site (STS) markers associated with FHB resistance in the two QTL regions identified in the first experiment were then used to characterize FHB QTL marker haplotypes and their effect on FHB resistance in seventy wheat genotypes. Five main haplotype groups (1-5) were characterized among the elite lines on the basis of allelic differences of four marker loci linked to the 3BS QTL and two marker loci linked to the 5AS QTL. Haplotype group 5 was comprised of marker allele combinations of both 3BS and 5AS QTL and elite lines with this haplotype have improved type I and type II resistance compared to the other haplotypes. This again validated the presence of QTL on chromosomes 3BS and 5AS, and illustrated the utility of SSR and STS markers in the two QTL regions in selection of FHB resistance in elite backgrounds. Four favorable marker alleles including two (Xbarc133 and XSTS3B142) on 3BS and two (Xbarc117 and Xbarc056) on 5AS are recommended for MAS of the two QTL for improved FHB resistance in wheat. Wheat lines having favorable marker alleles identified in the current study will provide breeding programs with a source of unique and adapted FHB resistant parents and some of the lines also may have potential for release as cultivars. / Ph. D.

Fusarium Head Blight (FHB) is a devastating fungal disease of wheat (Triticum aestivum L.) and results in significant economic losses due to reductions in grain yield and the accumulation of mycotoxins, such as deoxynivalenol (DON) and nivalenol (NIV). As a result, breeding programs have been working to identify resistance genes in wheat varieties known to be resistant to FHB. Some of the major quantitative trait loci (QTL) for FHB resistance identified to date have been from exotic sources such as 'Sumai3' and the Chinese landrace Wangshuibai, and native resistance has been identified in North American cultivars such as Ernie and Truman which are being used in breeding programs. This study was conducted to characterize and map QTL for resistance to FHB in the soft red winter wheat cultivar Jamestown and to identify tightly linked DNA markers associated with those QTL so that marker-assisted selection (MAS) can be used in pyramiding these and other known QTL into elite backgrounds. Types of resistance assessed in this study include: Type I (resistance to initial infection; incidence), Type II (resistance to spread in wheat spike; severity), and decreases in mycotoxin accumulation (DON) and percentage of Fusarium damaged kernels (FDK). A population composed of 186 F5:7 recombinant-inbred lines (RILs) from the cross Pioneer Brand '25R47'/Jamestown were used to evaluate these traits in six environments (MD, NC, and VA in 2011 and 2012). This study identified a QTL for resistance to DON accumulation and FHB severity on the wheat chromosome 1B. The QTL accounted for 12.7% to 13.3% of the phenotypic variation in DON accumulation and 26.1% of the phenotypic variation in FHB severity. The most diagnostic marker for the QTL on chromosome 1B associated with resistance to FHB severity and DON accumulation is Xwmc500.6 located 7.2 cM from the QTL peak and flanked by markers Xwmc500.7 and Xgwm273.2 (28.2 cM interval). / Master of Science

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, is a devastating fungal disease that affects barley production worldwide through damaged kernels, low yields, and production of mycotoxins. The most effective means of control is through the use of FHB resistant cultivars that are developed through gene pyramiding and incorporation of various sources of resistance. Resistance identified in winter barley cultivar Eve has been identified in Virginia Tech's Small Grains Breeding Program. The objectives of this study are to validate resistance and identify additional resistance QTL, and identify tightly linked and diagnostic markers for use in MAS programs. A population of F5:7 RILs derived from the cross Eve/Doyce were evaluated for FHB resistance. FHB incidence (Inc), FHB severity (Sev), Fusarium damaged kernels (FDK), and deoxynivalenol (DON) were assessed over 2014-15 and 2015-16 at Blacksburg, VA, Mount Holly, VA, Kinston, NC, and Lexington, KY. A QTL on chromosome 6H associated with FHB Sev, FDK, and DON was identified. The QTL accounted for as high as 14.5% of the phenotypic variation for DON accumulation, 8.3% for FHB Sev, and 11.87% to 17.63% for FDK. The QTL marker region spans 56.5 to 66.6 cM with flanking markers SCRI_RS_147342 and Bmag0613. QTL for morphological traits, heading date and height, were found in the same region as the FHB resistance traits. Diagnostic SNP makers associated with the FHB resistance QTL identified can be used for FHB resistance identification in MAS breeding programs to incorporate and pyramid resistance QTL and genes into other plant material. / Master of Science

All-male fry are preferred to prevent uncontrolled reproduction before harvest in intensive Nile tilapia (Oreochromis niloticus) aquaculture. Males also grow faster than females. An alternative approach to direct hormonal masculinisation of tilapia fry is to produce fry that are genetically male. However, sex determination system in tilapia is fairly complex. Recent developments have resulted in a linkage map and genetic markers that can be used to analyse the sex determination system. To analyse the genetic sex determination mechanism and to develop marker-assisted selection in the Stirling Nile tilapia population, a fully inbred line of clonal females (XX) was verified using test crosses and DNA markers (mostly microsatellites) to use as a standard reference line in sex determination studies. A series of crosses were performed involving this line of females and a range of males. Three groups of crosses were selected (each group consisted of three families) from progeny sex ratio distributions, and designated as type ‘A’ (normal XY males x clonal XX females), type ‘B’ (putative YY males x clonal XX females) and type ‘C’ (unknown groups of males x clonal XX females), for sex linkage study. For type ‘A’, inheritance of DNA markers and phenotypic sex was investigated using screened markers from tilapia linkage group 1 (LG1) to confirm the LG1-associated pattern of inheritance of phenotypic sex and the structure of LG1. Screened markers from LG1, LG3 and LG23 were used to investigate the association of markers with sex in families of type ‘B’ and ‘C’. In addition, a genome-wide scan of markers from the other 21 LGs was performed to investigate any association between markers and sex, in only families of cross type ‘B’. LG1 associated pattern of inheritance of phenotypic sex was confirmed by genotype and QTL analyses in families of cross type ‘A’. Analyses of genotypes in families of type ‘B’ and ‘C’ showed strong association with LG1 markers but no association with LG3 and LG23 markers. Genome wide scan of markers from all other LGs did not show any significant association between any markers and the sex. The allelic inheritance of two tightly linked LG1 markers (UNH995 and UNH104) in families of type ‘B’ and ‘C’ identified polymorphism in the sex determining locus: one of the alleles was associated mostly with male offspring whereas another allele was associated with both progeny (mostly males in type ‘B’ families, and approximately equal numbers in type ‘C’ families). This knowledge was used to identify and separate supermales (‘YY’ males) that should sire higher proportions of male progeny, reared to become sexually mature for use as broodstock. Two of them were crossed with XX females (one clonal and one outbred) to observe the phenotypic expression of the strongest male-associated allele in progeny sex. The observations of 98% male (99 males out of 101 progeny) and 100% male (N=75) from these two crosses respectively, suggest that a marker-assisted selection (MAS) programme for genetically male Nile tilapia production could be practical. This study also suggests that the departures from the sex ratios predicted using a “simple” XX/XY model (i.e., YY x XX should give all-male progeny) were strongly associated with the XX/XY system, due to multiple alleles, rather than being associated with loci in other LGs (e.g., LG3, LG23). This study also tentatively names the allele(s) giving intermediate sex ratios as “ambivalent” and emphasizes that the presence and actions of such allele(s) at the same sex-determining locus could explain departures from predicted sex ratios observed in some earlier studies in Nile tilapia.

A disponibilidade de informações baseadas nos marcadores genéticos surgiu como oportunidade de aprimorar os programas de melhoramento animal pela incorporação desses efeitos nas avaliações genéticas. Nesse contexto, o presente estudo teve como objetivos comparar modelos que consideraram ou não os efeitos dos marcadores para a estimação dos valores genéticos dos animais, bem como estimar os efeitos de substituição alélica dos marcadores por seis metodologias distintas (regressão múltipla bayesiana, regressão de cumeeira bayesiana, Bayes A, Bayes B, Bayes C&pi; e LASSO bayesiano) e avaliar o impacto da inclusão desses efeitos na acurácia das estimativas dos valores genéticos e os conflitos de seleção existentes aos serem comparadas as classificações dos animais com base nos valores genéticos clássicos e nos valores genéticos assistidos por marcadores. Dados de 83.404 animais pertencentes a um programa de seleção de animas da raça Nelore, mensurados para peso na desmama, ganho de peso pós-desmama, perímetro escrotal e escore de musculosidade, que corresponderam a 116.652 animais na matriz de parentesco, foram utilizados. Do total de animais com informações fenotípicas e genealógicas disponíveis, apenas 3.160 foram genotipados para 106 marcadores do tipo SNP. Os resultados obtidos para a comparação de modelos não demonstraram vantagens claras da inclusão conjunta dos efeitos poligênicos e dos marcadores nos modelos de avaliação genética, entretanto, os modelos que incluíram apenas o efeito dos marcadores tiveram os piores ajustes e desempenhos preditivos. As diferenças observadas entre as estimativas dos efeitos de substituição alélica dos marcadores pelas diferentes metodologias analisadas se devem à maneira como cada método regulariza esses efeitos. A incorporação das informações dos marcadores nas avaliações genéticas proporcionou, no geral, um aumento na acurácia das estimativas dos valores genéticos, especialmente para os tourinhos de reposição. Ao serem comparados os 20% melhores animais classificados com base no valor genético clássico e no valor genético assistido por marcadores, os maiores conflitos de seleção foram observados para os touros e tourinhos genotipados. Em suma, o presente projeto demonstrou que, embora a utilização de painéis de marcadores de muito baixa densidade não altere a capacidade preditiva dos modelos de avaliação genética, esses têm impacto na acurácia das estimativas dos valores genéticos. / The availability of molecular markers information turned out to be an opportunity to improve animal breeding programs, by the inclusion of those effects in the estimation of breeding values. Under that perspective, the aims of present research were to compare genetic evaluation models that assumed or not markers effects on the estimation of breeding values, as well estimate the allelic substitution effects of SNP markers applying six different methodologies (Bayesian multiple regression, Bayesian ridge regression, Bayes A, Bayes B, Bayes C&pi; and Bayesian Lasso) and evaluate the impact of these effects on the reliability of breeding values and the divergences on animals classification based on classical breeding values and marker assisted breeding values. Data of 83,404 animals belonging to a Nellore beef cattle (Bos indicus) selection program, measured for post-weaning gain, scrotal circumference and muscle score, corresponding to 116,562 animals on the relationship matrix, were used. From those animals, a set of 3,160 animals with phenotypic and genealogy data available, was genotyped for a panel of 106 SNP markers. Model comparison results did not demonstrate clearly the advantage of assuming polygenic and markers effects together in genetic evaluation models, however, models that considered only markers effects presented the worst global fit and predictive ability. Differences observed on the markers effects estimates were due the shrinkage process applied by each method. The incorporation of markers information on genetic evaluations provided, in general, increases on the reliability of breeding values, mainly for replacement young animals. Comparing the 20% best animals classified by classical breeding value and marker assisted breeding value, the highest divergences were observed to sires and young bulls that were genotyped. Summarizing, although this research showed that the inclusion of very low density SNP chip information was not able to improve the predictive ability of genetic evaluation models, they increased the reliability of breeding values estimates.