Karyotyping and Comparative Genomic Studies of Peanut and Its Wild Relatives

• Main Author: Zhang, Laining
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2013
• Subjects: Botany; Genetics; Molecular biology; Plant biology
• ISBN: 1303785315; 9781303785313

Peanut is native to southern America, but now it becomes the fourth-largest oil-seed crop. Total global peanut production is close to 35.5 million tons each year with China as the largest producer, followed by India and USA. Peanut can be directly consumed or made into vegetable oil and peanut butter. Additionally, peanut can be used to produce make-up, medicines and textile materials. The importance and popularity of peanut make it necessary for scientific studies. The cultivar peanut, Arachis hypogaea (AABB, 2n = 40), is an allotetraploid. It was originated from hybridization of Arachis. duranensis (AA) and Arachis. ipaensis (BB) followed by chromosome doubling. The wild species in the Arachis section are useful genetic resources due to presence of genes that confer biotic and abiotic stress resistance. However, the resource is not well exploited because little comparative genome studies between cultivated peanut and its wild relatives were performed. Characterization of its chromosome components will contribute to comparative genome studies. But the paucity of information on the DNA sequence and the presence of morphologically similar chromosomes make it difficult to construct a detailed karyotype for peanut chromosome identification. Tetraploid peanut and an A genome Cot-1 library were constructed to isolate highly and moderately repetitive sequences. Chromosomal distributions of these repeats were also investigated. Both genome and chromosome specific markers were identified. They can distiguish A and B genomes in tetraploid peanut and be used to construct a complete karyotyping of peanut chromosomes by FISH. In particular, a 115-bp tandem repetitive sequence was identified to be a B genome centromere repetitive DNA by immunofluoresence, mainly localized in the centromeres of B chromosomes, and a partial retrotransposable element was also identified at the centromeres of B chromosomes. Another 317 tandem repetitive sequence overlapped with A genome specific heterochromatin band in FISH, which was also found to be an A genome centromere repetitive DNA by immunofluoresence. These two tandem repetitive sequences, together with rDNA (5S, 45S), Arabidopsis telomere and three chromosome specific BAC clones were made probe cocktail, which can identify all 20 pairs of chromosomes in peanut and construct a complete karyotype. Karyotype analysis among three species support proveious report that A. duranensis and A. ipaënsis are ancestor of A. hypogaea. It also suggested that occurance of chromosome inversion might lead to accumulation of Arabidopsis telomere in the intercalary region of chromosome in A. hypogaea during evolution. Comparison of centromere DNA and CenH3 gene among three species suggested that centromere DNA show high variation and CenH3 gene highly conserved during evolution. The karyotyping of peanut is the first step for the construction of peanut physical map, and may provide a reference tool for the genome sequence assembly. It also makes it possible to study peanut chromosome structure and behavior, the evolution of peanut, and the use of wild species in peanut breeding. Additionally, the isolation of CenH3 gene which is an epigenetic centromere marker will facilitate identification of fuctional centromere and centromere evolution in peanut.