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Item Analysis of Genetic Diversity and Relationships in the China Rose Group(2011-02-22) Soules, Valerie AnnThe wild origin, early breeding history, and diversity of the China Rose group, including R. chinensis and its varieties, cultivars, and hybrids, are largely unknown. The aims of this study were to investigate the genetic diversity and relationships of the China Roses with related species and hybrids, including information in support of, or refuting, the hypothesis that these roses are the hybrid result of the wild R. chinensis var. spontanea and R. odorata var. gigantea. Ninety Rosa accessions, including China Roses, a Miscellaneous Old Garden Rose, Noisettes, early Polyanthas, Bourbons, Teas, and species from Sections Indicae and Synstylae were surveyed using 23 microsatellite primer pairs. The trnH-psbA chloroplast intergenic spacer was also sequenced for the China Roses, Misc. Old Garden Rose, and the species to look specifically at maternal relationships. A total of 291 alleles were scored for the 23 microsatellites, with alleles per locus ranging from 6-22 and averaging 12.65. A dendrogram based on Dice similarity and a three-dimensional Principle Coordinate Analysis (PCoorA) graph were plotted with the data. In the cluster analysis, the similarity coefficients ranged from ~0.15-0.99, with the cultivated roses forming well-defined groups at about 0.45 similarity. These groups generally reflected the American Rose Society horticultural classifications. A large number of sports and synonyms in the China Rose group were identified through this analysis as well. The PCoorA gave a better graphical representation of the relationships of the species and cultivars, and with the inclusion of the chloroplast sequence haplotypes, some maternal relationships could also be identified. This study shows that the cultivated China Roses are a closely related group and identified which accessions were likely Hybrid China Roses. The results also suggest that the China Roses were maternally derived from R. chinensis var. spontanea. Based on the microsatellites and chloroplast sequence haplotypes, the identity of the R. odorata var. gigantea accessions in this study are suspect, but the China Roses may also have this species in their background as the result of natural or artificial hybridization.Item Characterization of a gene from breeding line WX93D180 conferring resistance to leaf rust (Puccinia triticina) in wheat(2009-05-15) Hung, Hsiao-YiWheat (Triticum aestivum L. em. Thell, 2n=6x=42, AABBDD) is subjected to significant yield losses by the endemic leaf rust pathogen, Puccinia triticina (Roberge ex Desmaz. F. sp. tritici). Breeding for resistance to this disease is a more appropriate option both environmentally and economically over fungicidal application. More than 57 leaf rust resistance genes in wheat have been identified and many of the resistance genes have been successfully introgressed into resistant cultivars, yet the continuous shifting of predominant races of P. triticina continues to be a challenge to breeders. Pyramiding multiple resistance genes into a single resistant cultivar is one of the preferred strategies to develop superior disease resistant cultivars. Efficient pyramiding requires the utilization of markers closely linked to the resistance genes. The objectives of this study were to characterize a novel source of resistance to leaf rust introgressed into the breeding line WX93D180-R-8-1, to determine its inheritance, map position, and linkage with molecular markers suitable for marker assisted selection. According to the pedigree of WX93D180, TX86D1310*3/TTCC417, the resistance in this breeding line should be derived from TTCC417 (Turkey tritici cereal collection), which was thought to be Triticum monococcum, which is a diploid species made up of only the A genome. However, our marker analyzes results indicated the resistance gene is located in the D genome and has the same location as the cloned leaf rust resistance gene Lr21. We verified the result in our population using primers from Lr21 and found the same segregation pattern with the phenotypic data (disease response). Therefore the pedigree is incorrect, TTCC417 was misidentified, or the resistance was not from TTCC417.Item Construction of the Diploid, Tetraploid and Integrated Diploid-tetraploid Genetic Linkage Maps in Roses Using Simple Sequence Repeat (SSR) Markers(2014-01-03) Tsai, Ching-JungThis study uses polymorphic microsatellites (SSR) to elucidate the similarities among the diploid and tetraploid rose genomes by comparing their maps and clarifying the predominant inheritance patterns (disomic versus tetrasomic) seen in the tetraploid population. One hundred and eight out of 175 SSRs were polymorphic in both the OBxWOB26 (Old Blush x (?Basye?s Thornless? x ?Old Blush?) diploid backcross population and the GGFC (?Golden Gate? x ?Fragrant Cloud?) tetraploid full-sib population. Of these 69 fluorescently labeled SSRs and 5 morphological traits were used which generated 107 loci and 5 trait loci with 99 diploid population progeny. The tetraploid map was constructed with SSRs and AFLPs with 131 tetraploid progeny using the single dose restriction fragment (SDRF) analysis. The degree of preferential chromosome pairing in the tetraploid population was examined by looking at the segregation ratios among the double-dose markers (DDMs) as well as the ratio of loci in repulsion vs coupling phase using single-dose markers (SDMs). These approaches showed that there was a combination of disomic and tetrasomic inheritance. A diploid, a tetraploid and an integrated diploid-tetraploid genetic linkage map were developed from two populations using JoinMap 4 with the cross pollination option. In the diploid map, 7 integrated linkage groups covered a length of 352.3 cM with an average chromosome size of 50.3 cM. The morphological traits, prickles on stem (prickles), recurrent bloom (RB)) and flower type (Blfo) were mapped on the Chr LG3 which matched with the ICM (Integrated consensus map) published by Spillers et al., (2010). Moreover, 5 out of the 69 SSR markers (RhJ404, H9_B01, RW11E5, RW8B8 and RhE3) were mapped to two or more loci each on different chromosomes of the diploid map. In the tetraploid map, 174 out of 346 (50%) loci of single-dose markers (SDMs) and double-dose markers (DDMs) were mapped on a length of 883.4 cM with 9 linkage groups. Sixty anchor SSR markers were used to join the diploid and tetraploid maps which included 215 loci with a map length of 632 cM. Synteny of common SSRs and morphological traits, prickles, RB, Blfo, powdery mildew resistance (PM) and petal number (PN) on the integrated diploid-tetraploid map with the ICM, the GGFC and the K5 map demonstrated the collinear alignment among these maps.Item Diversity of Low Chill Peaches (Prunus persica) from Asia, Brazil, Europe and the USA(2011-08-08) Anderson, Natalie A.One hundred fifty-five peach (Prunus persica) cultivars, from Asia, Brazil, Europe, and the USA, were examined using eleven Simple Sequence Repeats (SSRs) to study the genetic relationships among low chill as compared to high chill peach germplasm. Data was analyzed by NTSYSpc to form a similarity matrix using Nei and Li?s Dice similarity coefficient. This similarity matrix was then subjected to a cluster analysis and a dendrogram was constructed using the UPGMA (Unweighted Pair-Group Method, Arithmetic Mean) method. A wide range of diversity was detected, from 0.33 coefficient of similarity amongst the Thai peaches to 0.97 between two Brazilian peaches. The most distant clusters were the low chill peaches from Thailand and Taiwan and the local cultivars (both fruit and ornamental types) from China. Among the improved germplasm, there were distinct clusters for the Chinese/Japanese cultivars, three clusters for the Brazilian cultivars and one for the cultivars from the USA and Europe. The Brazilian materials clustered according to breeding programs in S?o Paulo and Pelotas reflecting the different sets of local cultivars used in the breeding efforts. The largest group investigated was the European/USA peaches. This group subdivided into three distinct clusters, with a general clustering of the low chill germplasm. The low chill accessions from Asia were genetically distant from the improved low chill peaches from the USA or Brazil. The low chill peaches from the Americas were more closely related to the high chill peaches developed in the USA and China/Japan due to the introgression of this germplasm into a low chill background.Item Evaluation of short-day onion doubled haploid lines(2009-05-15) Walker, Ryan LeeMolecular marker analysis of seven putative onion (Allium cepa) doubled haploid (DH) lines developed at Texas A&M University was conducted to verify genetic homozygosity. Analysis was also conducted on five equivalent conventional inbred lines, breeding lines developed from the same parental crosses as the DH lines, and the original parent lines. The markers have revealed polymorphisms within the parental lines and the conventional inbreds, but not in the DH lines. We can conclude therefore that these seven lines are true DH lines. Performance of these DH lines was tested in two field locations and compared to commercial check lines. Bulbs from the various crosses were evaluated for eight bulb traits: diameter, height, centers/bulb, ring thickness, number of rings/bulb, bulb weight, soluble solids content, and pungency. Some crosses were detected that yielded significantly greater bulb weight than the check lines. However, these lines also had significantly greater numbers of centers per bulb. To test how these lines would perform in a breeding program, two full diallel analyses were conducted according to Griffing?s Model I, Method 1. The first consisted of a four parent diallel cross using two red DH lines and two yellow DH lines. Bulbs from the various crosses were evaluated for the same eight bulb traits mentioned above. Significant variation was detected for genotypic, general combining ability (GCA), specific combining ability (SCA), reciprocal (REC), maternal (MAT), and nonmaternal (NMAT) effects for all traits except number of rings/bulb, soluble solids content, and pungency. Significant environmental effects were only detected with number of centers per bulb. The second diallel analysis, a four parent diallel with two DH lines and two inbred lines from the breeding program, showed significant variation for the same effects for all traits except soluble solids content. Generally, GCA effects were more important than SCA effects in explaining the variation observed between crosses. For all traits GCA and SCA were always larger than the reciprocal effects (divided into maternal and nonmaternal components).Item Expression of defense genes in sorghum grain mold and tagging and mapping a sorghum anthracnose resistance gene(2009-05-15) Katile, Seriba OusmaneSorghum grain mold and anthracnose are two major diseases of sorghum (Sorghum bicolor) that constrain sorghum production worldwide. Grain mold is caused by several species of fungi, but the two most common are Curvularia lunata and Fusarium thapsinum. Isolates of these two species were used to inoculate panicles of selected sorghum cultivars in green house and field experimentations. Panicles were sprayed at the time of anthesis with conidial suspensions of the two fungal species individually or in a mixture and with water to serve as a control. Samples were collected 48 hours after inoculation for RNA extraction. In greenhouse studies, four cultivars (Tx2911, Sureno, SC170 and RTx430) were used while thirteen cultivars were grown in the field experiments. Gene expression was measured for the following genes using real time polymerase chain reactions (rt-PCR): PR10, ?-glucanase, chitinase, thaumatin, sormatin, phenyalanine ammonia lyase (PAL), obtusifoliol 14?-demethylase (Obtus), antifungal protein (AFP), apoptosis related protein (Apop) and leucine rich repeat (LRR). Seed germination tests in field grown cultivars indicated that germination rates for SC279-14E, SC660 and Sureno were not greatly influenced by grain mold. Covering the panicles with bags served to protect them against grain mold pathogens. The seed mycoflora test showed that Fusarium thapsinum was the most frequently recovered species and there were more species present in non-covered panicles. The response of sorghum cultivars to grain mold infection involves multiple defense genes. Real time PCR used to study the expression of sorghum defense in greenhouse grown plants showed that mRNA encoding PR-10, a small 10 kDa protein, was highly expressed in the glumes and spikelets of resistant cultivars Tx2911 and Sureno and constitutively in leaves. The expression of some other defense genes like beta-glucanase, chitinase and AFP was variable. Sormatin was not expressed. Expression of ?-glucanase, chitinase, and PR10 was higher in field than in greenhouse experiments. A second area of research involved tagging of a resistance gene for sorghum anthracnose. Three AFLP markers (Xtxa607, Xtxa3181 and Xtxa4327) and three SSRs (Xtxp3, Xtxp55 and Xtxp72) were identified. These markers were loosely linked to the resistance genes. The markers are located on linkage group B. The results suggest that markers located 20-30 cM on one side or the other of those tested should provide useful tags for the resistance gene.Item IDENTIFICATION OF DROUGHT-RELATED QUANTITATIVE TRAIT LOCI (QTLs) IN SUGARCANE (Saccharum spp.) USING GENIC MARKERS(2011-08-08) Sharma, VivekPopulation based association studies in crops that were established by domestication and early breeding can be a valuable basis for the identification of QTLs. A case control design in a population is an ideal way to identify maximum candidate sites contributing to a complex polygenic trait such as drought. In the current study, marker loci associated with drought related QTLs were identified in sugarcane (Saccharum spp), one of the most complex crop genomes, with its polyploid nature (>8), chromosome number (>100) and interspecific origin. The objectives of this investigation were: 1) development of genic markers, which can be used for marker-assisted selection of drought tolerant genotypes of sugarcane. 2) genotypic characterization of sugarcane population at drought related loci using EST-SSR markers. Using 55 microsatellite markers, 56 polymorphisms were scored among 80 modern sugarcane genotypes. Homogeneity of the population was confirmed by determining the distribution of allele frequencies obtained by random genomic microsatellite markers. This analysis was conducted in the STRUCTURE program and the population was divided in 3 subgroups based on the allelic distribution. Phenotypic data to evaluate drought tolerance among the genotypes was collected by measuring chlorophyll content, chlorophyll fluorescence, leaf temperature and leaf relative water content. A generalized linear model in SPSS was used to find association between marker loci and phenotypic data. Markers with significant association (P 0.001 level) with the trait were subjected to linear regression to screen the spurious associations. Based on the results, 21 EST-SSR markers and 11 TRAP markers related to drought-defining physiological parameters were considered as genuine associations in this study. Fifty-six polymorphisms produced by 13 EST-SSR primers were used to produce genetic similarity matrix for 80 genotypes. Dendrogram prepared from this genetic similarity matrix will be useful in selecting parents carrying diversity at drought specific loci.Item Quantitative trait loci affecting the agronomic performance of a Sorghum bicolor (L.) Moench recombinant inbred restorer line population(Texas A&M University, 2004-09-30) Moran Maradiaga, Jorge LuisLately the rate of genetic gain in most agronomic crop species has been reduced due to several factors that limit breeding efficiency and genetic gain. New genetic tools and more powerful statistical analyses provide an alternative approach to enhance genetic improvements through the identification of molecular markers linked to genomic regions or QTLs controlling quantitative traits. The main objective of this research was to identify genomic regions associated with enhanced agronomic performance in lines per se and hybrid combination in Sorghum bicolor (L.) Moench. A population composed of 187 F5:6 recombinant inbred lines (RIL) was derived from the cross of restorer lines RTx430 and RTx7000. Also, a testcross hybrid population (TCH) was developed by using each RIL as a pollinator onto ATx2752. A linkage map was constructed using 174 marker loci generated from AFLP and SSR primer combinations. These markers were assigned to 12 different linkage groups. The linkage map covers 1573 cM with marker loci spaced at an averaged 9.04 cM. In this study, 89 QTL that control variation in seven different morphological traits were identified in the recombinant inbred line population, while in the testcross hybrid population, 79 QTL were identified. These traits included grain yield, plant height, days to mid-anthesis, panicle number, panicle length, panicle exsertion and panicle weight. These putative QTL explained from 4 to 42% of the phenotypic variation observed for each trait. Many of the QTL were not consistent across populations and across environments. Nevertheless, a few key QTL were identified and the source of the positive additive genetics isolated. RTx7000 was consistently associated with better agronomic performance in RIL, while in testcrosses, RTx430 was. Some genomic regions from RTx7000 may be utilized to improve RTx430 as a line per se. However, it is very unlikely that such regions will have a positive effect on the combining ability of RTx430 since testcross results did not reveal any transgressive segregants from the RIL population.