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High‐throughput development of SSR marker candidates and their chromosomal assignment in rye ( Secale cereale L.)
Author(s) -
Li Jianjian,
Zhou Ruonan,
Endo Takashi R.,
Stein Nils
Publication year - 2018
Publication title -
plant breeding
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.583
H-Index - 71
eISSN - 1439-0523
pISSN - 0179-9541
DOI - 10.1111/pbr.12619
Subject(s) - secale , biology , genetics , primer (cosmetics) , chromosome , in silico , genetic marker , common wheat , transferability , microsatellite , molecular marker , triticeae , gene , genome , botany , allele , chemistry , statistics , mathematics , organic chemistry , logit
Shotgun survey sequences of flow‐sorted individual rye chromosomes were data mined for the presence of simple sequence repeats ( SSR s). For 787,850 putative SSR loci, a total of 358,660 PCR primer pairs could be designed and 51,138 nonredundant SSR marker candidates were evaluated by in silico PCR . Of the 51,138 SSR primer candidates, 1,277 were associated with 1,125 rye gene models. A total of 2,112 of the potential SSR markers were randomly selected to represent about equal numbers for each of the rye chromosomes, and 856 SSR s were assigned to individual rye chromosomes experimentally. Potential transferability of rye SSR s to wheat and barley was of low efficiency with 4.3% (2,189) and 0.4% (223) of rye SSR s predicted to be amplified in wheat and barley, respectively. This data set of rye chromosome‐specific SSR markers will be useful for the specific detection of rye chromatin introgressed into wheat as well as for low‐cost genetic and physical mapping in rye without the need for high‐tech equipment.