Development and Application of EST-Based Markers Specific for Chromosome Arms of Rye (<i>Secale cereale</i> L.)

Abstract

To develop a set of molecular markers specific for the chromosome arms of rye, a total of 1,098 and 93 primer pairs derived from the expressed sequence tag (EST) sequences distributed on all 21 wheat chromosomes and 7 rye chromosomes, respectively, were initially screened on common wheat ‘Chinese Spring’ and rye cultivar ‘Imperial’. Four hundred and fourteen EST-based markers were specific for the rye genome. Seven disomic chromosome addition lines, 10 telosomic addition lines and 1 translocation line of ‘Chinese Spring-Imperial’ were confirmed by genomic in situ hybridization and fluorescencein situ hybridization, and used to screen the rye-specific markers. Thirty-one of the 414 markers produced stable specific amplicons in ‘Imperial’, as well as individual addition lines and were assigned to 13 chromosome arms of rye except for 6RS. Six rye cultivars, wheat cultivar ‘Xiaoyan 6’ and accessions of 4 wheat relatives were then used to test the specificity of the 31 EST-based markers. To confirm the specificity, 4 wheat-rye derivatives of ‘Xiaoyan 6 × German White’, with chromosomes 1RS, 2R and 4R, were amplified by some of the EST-based markers. The results indicated that they can effectively be used to detect corresponding rye chromosomes or chromosome arms introgressed into a wheat background, and hence to accelerate the utilization of rye genes in wheat breeding.

High‐throughput development of SSR marker candidates and their chromosomal assignment in rye (Secale cereale L.)

“…In total, 856 of 2,112 SSR primers produced expected single PCR products both in the euploid rye and in the corresponding CS‐rye addition and substitution lines. This success rate (40.5%) was higher than reported in other studies that had attempted to acquire rye chromosome‐specific markers directly from wheat and rye expressed sequence tag (EST) primers; for example, a success rate of 7.5% (31/414) was reported based on screening EST sequences distributed on all 21 wheat chromosomes and seven rye chromosomes (Xu et al., ). A comparable success rate (55.0%) was achieved in a study using the PLUG (PCR‐based landmark unique gene) marker system (Li, Endo, et al., ), in which rye chromosome‐specific markers were developed from wheat PLUG markers, that is, EST‐PCR markers developed based on the orthologous gene conservation between rice and wheat (Ishikawa, Yonemaru, Saito & Nakamura, ).…”

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

“…This demonstrated that some rye chromosome-specific markers are not able to identify a given chromosome across all rye cultivars. In most of the previous studies, researchers usually developed rye-specific markers basing on the obtained sequences from one kind of rye cultivar or only used one set of wheat-rye addition lines to assign them, without confirming their universality in many other rye cultivars [24,25,[43][44][45]. In the present study, a total of 404 PCRbased rye chromosome-specific markers were developed based on the conserved sequence across the five rye cultivars and verified with the sixth rye cultivar KingII.…”

“…d ND-FISH analysis of same metaphase cell with after GISH analysis (c) with Oligo-pSc119.2-1 (green) and Oligo-pAs1-1 (red). The bar represents 10 μm and the arrows represent rye chromosomes or chromosome arms 23,25,24,50,30,33,16,42,26, 37 markers were successively assigned to 1RS, 1RL, 2RS, 2RL, 3RS, 3RL, 4RS, 4RL, 5RS, 5RL, 6RS, 6RL, 7RS and 7RL arms of rye chromosome, respectively (Fig. 3).…”

“…Despite a series of rye-specific markers have been reported [24][25][26][27][28], it is still in a large demand when applied in highresolution mapping, population genetic studies and marker assisted selection (MAS). In addition, as a crosspollinated crop, rye contains significant genetic heterogeneity within and among cultivars [29,30].…”

Diversity resistance to Puccinia striiformis f. sp Tritici in rye chromosome arm 1RS expressed in wheat

“…The use of molecular markers was a fast way to indentify alien chromatin, but unstable. Up to now, many molecular markers have been developed, including the rye specific marker Pr20H, designed according to the rye-specific repetitive sequence of pSc20H (Fu et al, 2010), and specific markers of each rye chromosome arm (Xu et al, 2012;Tomita and Seno, 2012). Fu et al (2010) considered that the combination of molecular and cytological analysis could increase the efficiency of detecting alien chromatin introgressions.…”