| Dense genetic maps and quantitative trait loci(QTLs) detected on such maps are powerful tools for genomics and molecular breeding studies. Eucalyptus is a widely planted hardwood genus over the world. In this dissertation, we focus on the development of dense genetic maps and detection of economically important QTLs. Using multiple marker types including diversity array technology(DAr T), expressed sequence tag(EST), simple sequence repeats(SSR), insert-deletion(In Del), cleaved amplified polymorphic sequence(CAPS) and single nucleotide polymorphism(SNP), we developed dense genetic maps of E. urophylla and E. tereticornis and detected QTLs for growth, wood basic density and cellulose content. The main contents are as follows.(1) Preliminary detection of QTLs for growth and wood density in E. urophylla(Ur) and E. tereticornis(Te). The traits are height(H, m) measured at 10, 23, 32, 44 and 56 months of age(H10, H23, H32, H44 and H56, respectively), diameter at breast height(D, cm) measured at 23, 32, 44 and 56 months(D23, D32, D44 and D56, respectively) and wood density measured at 56 months(WD56). A total of 31 and 22 QTLs were detected in nine and four linkage groups(LGs) of E. urophylla and E. tereticornis dense genetic maps, respectively, which had been constructed mainly with DAr T markers in our laboratory. Twelve regions(six in each of Ur and Te) influenced multiple traits, reducing the total non-overlapping QTL regions to 27(15 in Ur and 12 in Te). One to four QTLs were identified for each trait on either of the maps, ranging in LOD score from 3.4 to 7.1. These QTLs explained between 8.3% and 18.9% of the total phenotypic variation in the respective traits. Growth and wood density QTLs were generally independent. Two to 560 positional candidate genes were observed for a QTL through aligning QTL confidence intervals with the E. grandis genome sequence.(2) Development of a novel set of 144 EST-In Del markers in Eucalyptus based on ESTs from Gen Bank. Amplicon sequencing against two parents of a mapping population(E. urophylla ? E. tereticornis) revealed that the In Del size ranged from 2 to 44 bases and the dinucleotide type was the most abundant(37.3%). The cross-species/subgenus amplification rate ranged from 62.5% in E. tessellaris(subgenus Blakella) to 99.3 % in E. grandis(subgenus Symphyomyrtus) with an average of 85.4 %. There were 121 EST-In Dels(84.0%) polymorphic among 12 individuals of E. grandis, and the number of alleles per polymorphic locus(Na), observed heterozygosity(Ho), expected heterozygosity(He) and polymorphic information content(PIC) were 2–12(mean 4.0), 0.0–1.0(mean 0.278), 0.083–0.892(mean 0.538) and 0.077–0.841(mean 0.465), respectively. Physical positions of 143 EST-In Dels were predicted on the E. grandis genome sequence. A total of 81 EST-In Dels were incorporated into prior dense genetic maps of E. urophylla and E. tereticonis, and extensive synteny and colinearity were observed between E. grandis genome sequence and the mapped markers.(3) Development of EST-SNP markers and construction of dense transcript linkage maps in Eucalyptus. Based on the ESTs downloaded from Gen Bank, more than 2300 EST-SNP markers were developed through direct amplicon sequencing against two parents of a mapping population E. urophylla ? E. tereticornis, 1536 EST-SNPs of which were included in design of a Golden Gate microarray. The microarray was then used to genotype the two parents and 896 sibs of the mapping population for purposes of dense transcript linkage map construction and economically important QTL detection.There were 1178(76.7%) EST-SNPs successfully genotyped with the Golden Gate microarray. Together with previously mapped EST-SSR, EST-In Del and EST-CAPS markers, those EST-SNPs were integrated into genetic maps of both parents. The final linkage map of maternal E. urophylla consisted of 641 EST markers(including 559 EST-SNPs) across 11 linkage groups(LGs), with a total map length of 1377.1 c M. The number of loci per LG varied from 29(Eu_LG7) to 72(Eu_LG3). The size of the LGs ranged from 80.3(Eu_LG7) to 161.8 c M(Eu_LG8), averaging at 125.1 c M per LG. The mean distance of marker interval was 2.2 c M, with a range between 0.04 c M(Eu_LG2) and 26.9 c M(Eu_LG7).The final linkage map of paternal E. tereticornis consisted of 699 EST markers(including 623 EST-SNPs) across 11 LGs, with a total map length of 1304.6 c M. The number of loci per LG varied from 38(Et_LG9) to 118(Et_LG6). The size of the LGs ranged from 85.6(Et_LG9) to 149.0 c M(Et_LG6), averaging at 118.6 c M per LG. The mean distance of marker interval was 2.1 c M, with a range between 0.03 c M(Et_LG8) and 27.4 c M(Et_LG6).High levels of synteny and colinearity were revealed between either of our maps and E. grandis genome sequence. Each of the LGs could be aligned to the respective main scaffold of E. grandis genome. The E.urophylla and E.tereticornis maps covered 564.6 Mb(93.2%) and 568.5 Mb(93.8%) of the E. grandis genome(605.8 Mb).(4) Detection of QTLs on the dense transcript linkage maps. QTLs related with 93-month-old height, diameter, wood basic density and cellulose content were detected separately with clonal(338 sibs) and seedling(558 sibs) phenotypes. A total of 10 QTLs were identified for the four traits on both parental linkage maps based on clonal performance, with LOD scores 3.4–8.4 and explaining 3.4–11.5% of the total phenotypic variation in the respective traits. A total of 15 QTLs were identified for all the traits based on seedling performance, with LOD scores 3.5–7.6 and each explaining 3.7–7.6% of the total phenotypic variation. However, there were no common QTLs for clonal and seedling traits, indicating that the major genes controlling the clonal and seedling phenotypes may be different. |
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