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

dc.contributor.advisor Steven B. Cannon
dc.contributor.advisor Thomas Lübberstedt
dc.contributor.author Belamkar, Vikas
dc.contributor.department Agronomy
dc.date 2018-08-11T07:03:24.000
dc.date.accessioned 2020-06-30T02:58:17Z
dc.date.available 2020-06-30T02:58:17Z
dc.date.copyright Thu Jan 01 00:00:00 UTC 2015
dc.date.embargo 2016-10-30
dc.date.issued 2015-01-01
dc.description.abstract <p>This dissertation has two main objectives: (1) morphological and genetic characterization of a little-studied edible legume native to North America, Apios americana; and (2) characterization of the soybean (Glycine max) homeodomain leucine zipper (HD-Zip) transcription factor family (involved in abiotic stress responses), and identification of candidate genes for dehydration and salt stress. In these projects, next generation sequencing (NGS) is evaluated as a tool for rapidly characterizing genetic variation (in Apios) and fine-scale genetic responses to abiotic stress (in soybean).</p> <p>Apios, commonly called “potato bean,” is a nitrogen-fixing legume that is adapted to diverse climatic conditions of central and eastern North America. It produces tubers (modified stem-tubers) that are rich in protein, have a long shelf life under refrigeration (>1 year), contain isoflavones, and have low levels of reducing sugars (potentially making the tubers useful for fried chips, for example). The plant was once a staple wild-collected food of Native American Indians, and is now a cultivated crop in Japan and South Korea. William J. Blackmon and Berthal D. Reynolds evaluated Apios as a new edible tuber crop in the US during the 1980s. Their breeding efforts during 1985-1994 lead to a collection of improved genotypes. As of 2010, 53 genotypes remained from Blackmon and Reynolds’ work. As part of this dissertation project, phenotypic evaluation of these 53 genotypes was performed for multiple years, in multiple environments (Iowa, Virginia and Pennsylvania), and in three growing conditions (field, 305-mm [12-in.] pots and 381-mm [15 in.] grow-bags). Twenty traits were recorded, including 10 aboveground and 10 belowground measurements. There was significant variation among the genotypes for all but two emergence traits. Several genotypes produced high yields - up to 1,515 g of tuber yield/plant. Transcriptome sequencing of multiple tissues from a single genotype generated both a high-quality de novo reference transcriptome assembly and an expression catalog. Re-sequencing of the leaf transcriptome from all the genotypes in the collection allowed identification of 58,154 high-quality SNPs and 39,609 gene expression markers (GEMs). Both SNPs and GEMs revealed population structure and pedigree relationships in the collection. Transcripts mapped to Phaseolus vulgaris (another legume in the Phaseoleae clade as Apios, with the same chromosome number and presumably similar genome structure) helped in building pseudo-Apios chromosomes. Linkage disequilibrium decay was investigated in the collection using putative genomic locations of the SNP markers, derived using the pseudo-Apios chromosomes. Association analysis conducted using SNPs and GEMs identified marker-trait associations for at least 11 traits. In summary, this study demonstrates accelerated and holistic (genomic and phenotypic) exploration of an underutilized crop.</p> <p>The HD-Zip transcription factor family includes genes involved in abiotic stress. HD-Zip genes are well characterized in Arabidopsis thaliana, but not yet in soybean. As part of this dissertation project, HD-Zip genes were identified in the soybean genome using homology searches and Hidden Markov Model guided sequence alignments. Phylogeny reconstruction enabled placement of HD-Zip sequences into four previously described subfamilies. Syntenic paralog pairs were retained following polyploidy in Glycine ~13 Mya. RNA-Seq analysis identified 20 differentially expressed HD-Zip genes in the roots of soybean cv. ‘Williams 82’, at least at one of the three time points (1, 6, or 12 hr) under dehydration and salt stress. This indicates the role of HD-Zip genes in abiotic stress responses. Expression profiles generated for genes expressed in roots at 0, 1, 6 and 12 hr under dehydration and salt stress will serve as an important resource for soybean genomic studies, and will aid in understanding plant responses to dehydration and salt stresses.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/etd/14662/
dc.identifier.articleid 5669
dc.identifier.contextkey 8052024
dc.identifier.doi https://doi.org/10.31274/etd-180810-4836
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath etd/14662
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/28847
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/etd/14662/0-Chapter2_SupplementaryFiles.zip|||Fri Jan 14 20:24:44 UTC 2022
dc.source.bitstream archive/lib.dr.iastate.edu/etd/14662/1-Chapter3_SupplementaryFiles.zip|||Fri Jan 14 20:24:26 UTC 2022
dc.source.bitstream archive/lib.dr.iastate.edu/etd/14662/2-Chapter4_SupplementaryFiles.zip|||Fri Jan 14 20:24:45 UTC 2022
dc.source.bitstream archive/lib.dr.iastate.edu/etd/14662/Belamkar_iastate_0097E_15022.pdf|||Fri Jan 14 20:24:48 UTC 2022
dc.subject.disciplines Agriculture
dc.subject.disciplines Botany
dc.subject.disciplines Computational Biology
dc.subject.disciplines Plant Breeding and Genetics
dc.subject.keywords Genetics and Genomics (Computational Molecular Biology)
dc.subject.keywords Genetics
dc.subject.keywords Genomics
dc.subject.keywords Genetics and Genomics
dc.subject.keywords Computational Molecular Biology
dc.subject.keywords Apios
dc.subject.keywords Apios americana
dc.subject.keywords Germplasm
dc.subject.keywords Phenotype
dc.subject.keywords Sequencing
dc.subject.keywords Soybean
dc.supplemental.bitstream Chapter2_SupplementaryFiles.zip
dc.supplemental.bitstream Chapter3_SupplementaryFiles.zip
dc.supplemental.bitstream Chapter4_SupplementaryFiles.zip
dc.title 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
dc.type article
dc.type.genre dissertation
dspace.entity.type Publication
relation.isOrgUnitOfPublication fdd5c06c-bdbe-469c-a38e-51e664fece7a
thesis.degree.discipline Genetics and Genomics (Computational Molecular Biology)
thesis.degree.level dissertation
thesis.degree.name Doctor of Philosophy
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