Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

Abstract

In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.

Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP

“…The bread wheat ( Triticum aestivum ) genome is 17 Gbp in size, around 6 times larger than the human genome [14], consists of 75%–90% repeats [15,16] and is hexaploid, containing of the A, B and D genomes, each with 7 homoeologous chromosomes. The presence of multiple genomes, large size and abundant repeats make any genetic and genomic analysis a challenge [17].…”

Development of a new set of molecular markers for examining Glu-A1 variants in common wheat and ancestral species

“…Xrj5 , Xrj6 and Xrj7 were three repeat DNA insertion site based polymorphism (ISBP) markers [41, 42]. Xrj5 was developed to diagnose the presence of an intact miniature inverted repeat transposable element ( Mite-5 ) in the ORF of the receptor kinase b gene in Renan, which was truncated in Langdon and absent in G1812 (Fig 1A, S3 Fig).…”

Multifactorial Mapping of QTL for Yield and Yield Component in Wheat (Triticum Aestivum) in Normal and Drought Conditions

“…Hexaploid wheat (2n = 6x = 42) has a large genome size of about 17300 Mb (Hussain and Rivandi, 2007). Repetitive DNA elements make for approximately 90% and transposable elements make up 80% of wheat genome (Wanjugi et al, 2009). Determining the number of controlling genes and them effect on qualitative traits such as yield and yield components are fundamental steps towards molecular breeding of crops (Cooper et ).…”