Development of a set of PCR markers specific to Aegilops longissima chromosome arms and application in breeding a translocation line

Abstract

Transcriptome data were used to develop 134 Aegilops longissima specific PCR markers and their comparative maps were constructed by contrasting with the homologous genes in the wheat B genome. Three wheat- Ae. longissima 1BL·1S S translocation lines were identified using the correspondence markers. Aegilops longissima is an important wild species of common wheat that harbors many genes that can be used to improve various traits of common wheat (Triticum aestivum L.). To efficiently transfer the traits conferred by these Ae. longissima genes into wheat, we sequenced the whole expression transcript of Ae. longissima. Using the transcriptome data, we developed 134 specific polymerase chain reaction markers located on the 14 chromosome arms of Ae. longissima. These novel molecular markers were assigned to specific chromosome locations based on a comparison with the homologous genes in the B genome of wheat. Annotation of these genes showed that most had functions related to metabolic processes, hydrolase activity, or catalytic activity. Additionally, we used these markers to identify three wheat-Ae. longissima 1BL·1SS translocation lines in somatic variation populations resulting from a cross between wheat cultivar Westonia and a wheat-Ae. longissima substitution line 1S(1B). The translocation lines had several low molecular weight glutenin subunits encoding genes beneficial to flour processing quality that came from Ae. longissima 1SS. The three translocation lines were also confirmed by genomic in situ hybridization. These translocation lines will be further evaluated for potential quality improvement of bread-making properties of wheat.

Discovery of powdery mildew resistance gene candidates fromAegilops biuncialischromosome 2Mbbased on transcriptome sequencing

“…Wang et al (2018) developed 134 Ae. longissima chromosome - specific markers by RNA-seq [30]. Li et al (2019) developed 76 molecular markers specific to the chromosome 1V to 7V of D. villosum #4 based on transcriptome data [31].…”

“…Furthermore, molecular markers of alien chromosome-specific were limited for fine mapping of alien genes. Regardless, with the rapid development of high-throughput sequencing, sequencing-based technologies such as RNA-seq have been frequently used to develop molecular markers [1,30,31], detect gene expression pattern and level responded to pathogens [32], exploit new genes and identify gene function without prior information of the particular reference genome [33,34]. RNA-seq is very helpful to explore disease-resistant genes (R) derived from wild relatives.…”

Physical Mapping of Pm57, a Powdery Mildew Resistance Gene Derived from Aegilops searsii

“…For example, Stpk-V, a putative serine/threonine-protein kinase gene derived from D. villosum against powdery mildew was successfully cloned and characterized based on integrating microarray analysis of transcriptomes before and after Bgt-inoculation with physical mapping of chromosomal segment locating Pm21 [44]. Further RNA-seq has also been used to develop molecular markers for diagnosing chromosomes, chromosome segments or genes in wild relatives [46,47].…”

Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines

“…Recently, RNA-seq has been frequently used to develop molecular markers specific to chromosomes of wild relatives of cultivated wheat. For example, Thinopyrum intermedia genome-specific EST-SSR markers, Agropyron cristatum chromosome 6P-specific EST markers, Aegilops longissima chromosome-arm specific PCR markers and D. villosum#4 chromosome 6V#4S-specific PCR markers were developed using transcriptome data [31, 41–43]. Thereby, RNA-seq is a potential strategy to develop molecular markers specific to different chromosome arms of wild species of wheat.…”