Phenotypic and genetic variation in an Apios americana breeding collection; and characterization of the HD-Zip gene family, involved in abiotic stress responses in Glycine max

Abstract

Variance components and broad-sense heritability of traits in field experiments…………………………………………………. 2.4.2 Variance components and broad-sense heritability of traits in pots and grow-bags experiments…………………………………. 2.4.3 Summary statistics of the traits evaluated on the Apios collection. 2.4.4 Phenotypic correlations among the above-and belowground traits iv 2.4.5 Phenotypic correlations among the four traits recorded in four environments……………………………………………………… 2.4.6 Rank correlations of the four traits recorded in four environments. 2.4.7 Hierarchical clustering analysis………………………………….... 2.4.8 Principal component analysis……………………………………… 2.4.9 Candidate genotypes and potential crossing schemes for developing the first cultivars of Apios…………………………….. 2.5 Acknowledgments…………………………………………………………… 2.6 References………………………………………………………………….... 2.7 Figures……………………………………………………………………….. 2.8 Tables………………………………………………………………………... CHAPTER 3. GENOMICS-ASSISTED CHARACTERIZATION OF A BREEDING COLLECTION OF APIOS AMERICANA, AN EDIBLE TUBEROUS LEGUME…… 52 3.1 Abstract……………………………………………………………………… 3.2 Introduction…………………………………………………………………. 3.3 Results………………………………………………………………………. 3.3.1 Development and evaluation of an Apios breeding collection………. 3.3.2 De novo transcriptome assembly, annotation and expression catalog. 3.3.3 Marker discovery, validation and genotyping of the collection……… 3.3.4 Diversity, inbreeding and pedigree in the collection………………… 3.3.5 Population structure of the collection………………………………… 3.3.6 Linkage disequilibrium (LD) in the collection………………………. 3.3.7 Marker-trait associations in the collection…………………………… 3.3.8 Marker-trait associations using gene expression markers (GEMs)….. 3.4 Discussion…………………………………………………………………… 65 3.5 Methods……………………………………………………………………… 3.5.1 Historical and morphological evaluation of the Apios americana collection……………………………………………………………… 3.5.2 De novo transcriptome assembly, annotation and expression catalog. 3.5.3 Genotyping of the collection using RNA-Seq……………………….. 3.5.4 Diversity estimates, inbreeding and pedigree in the collection……… v 3.5.5 Population structure of the collection………………………………… 3.5.6 Linkage disequilibrium (LD), and LD decay in the collection………. 3.5.7 Association analysis using SNP markers…………………………….. 3.5.8 Association analysis using gene expression markers………………... 79 3.6 Acknowledgments…………………………………………………………… 3.7 References………………………………………………………………….... 3.8 Figures………………………………………………………………………. 3.9 Tables……………………………………………………………………….. CHAPTER 4. COMPREHENSIVE CHARACTERIZATION AND RNA-SEQ PROFILING OF THE HD-ZIP TRANSCRIPTION FACTOR FAMILY IN SOYBEAN (GLYCINE MAX) DURING DEHYDRATION AND SALT STRESS…... 99 4.1 Abstract………………………………………………………………………. 4.2 Background…………………………………………………………………... 4.3 Methods……………………………………………………………………… 4.3.1 Homology searches, multiple sequence alignments, and phylogenetic analysis…………………………………………….. 4.3.2 Validation, structural characterization, and duplication history of HD-Zip genes……………………………………………………... 4.3.3 Expression profiles of HD-Zip genes in...

Genetic Transformation of LoHDZ2 and Analysis of its Function to Enhance Stress Resistance in Larch

“…Temperature stress includes high-temperature, low-temperature and severe variable-temperature stress [31] . HD-Zips are mostly studied under high-temperature and low-temperature stress [32] . Under these two stresses, most enzyme activities are decreased, resulting in abnormal biochemical reactions and possibly cell death [33] .…”