| Rye(Secale cereale L;2n=2x=14,RR)is a cross-pollinated crop with resistance for several biotic and abiotic stresses which represents an important genetic resource for wheat improvement.Rye has a large genome(-8Gb)which contains a large amounts of repeats such as tandem repeats of pSc200,pSc250 and pSc119.2.Repeat sequences variation play important roles in the evolution of rye chromosomes.In this study,22 oligoneucleotide probes were designed and 12 produced specific signals in rye chromosomes.Using two oligonucleotides TAMRA-oligo-6 and FAM-pSc 119.2-1 representing tandem repeats of pSc200 and pSc119.2,respectively,we analyzed a total of 4200 chromosomes of 300 plants from six open-pollinated rye varieties(Jingzhouheimai,Zhaotongheimai,Dongmu70,AR47,AR62 and HP).A total of 73 heterochromatin blocks(bands)were identified on all chromosomes,including 43 from pSc119.2 and 30 from pSc200.Among the 73 heterochromatin block types,8(10.96%)were completely conserved in different cultivars and individuals,and 65(89.04%)had variation ratesranging from 0.17%to 49.67%with an average of 14.47%.Block 6R-g3(49.67%)had the highest level of variation rate.The average variation rate of pSc200 on all chromosomes(19.33%)was higher than pSc119.2(11.08%),indicating pSc200 may have greater impact on rye evolution.322 polymorphic chromosomes(recombination of different heterochromatin block types)were identified,and 6R had the most polymorphic type(96),followed by 7R(58)>4R(45)>5R(38)>1R(30)>3R(28)>2R(27).Among these polymorphic chromosomes,14 were 5 times higher than the expected values which were defined as the main(advantage)types.Six preferentially transmitted chromosomes were confirmed by karyotype analysis in 40 wheat-rye F1 hybrid plants.Based on the heat map analysis of polymorphic chromosome types and amounts,the six rye varieties were clustered into three groups,of which AR47 belonged to group 1,JZHM with ZTHM belonged to group 2,and HP,DM70 and AR62 belong to group 3.Among the 300 plants investigated,63.00%to 86.66%heterozygosity,and 43.66%to 90.32%heterogeneity for each chromosome were observed.The results showed that the heterochromatin blocks variation and recombination between rye chromosomes resulted in abundant chromosome diversity.Compared with pSc119.2,pSc200 heterochromatin block variation seems playmore roles in the evolution of rye chromosomes.In order to transfer and utilize the beneficial genes of rye,12 structural variants were identified from F6 plants of Chinese Spring ph1bph1b×MA5R hybrids by fluorescence in situ hybridization(FISH)and genomic in situ hybridization(GISH),which involved translocations,addition and deletions.From the 270 F7 plants,150 plants were identified with structural variations,including 12 structural variant types.Based on the cytological results of F6 and F7,two structural variants(MtA5RL and T5AS-5AL-5RL#1)containing different 5RL chromosome segments were selected for further study.The 5RL was divided into 2 segments,which were named 5RL-1 and 5RL-2 from the centromere,respectively,and the hairy peduncle gene was located at 5RL-2.Using the rye and wheat reference genome sequences,251 pairs of IT primers were designed by alignment analysis,and amplification analysis was performed on Jingzhouheimai,Huixianhong,Jinghuil and MtA5RL,120 pairs of primers have specific ampliconsin Jingzhouheimai with polymorphism rate 47.81%.Each of 96 pairs of primers generated one to three specific sites in rye which were located in 5RL.The forementioned two variants were analyzed which enabled mapping 85 markers(80 newly developed IT markers and 5 pre-published markers in the laboratory)to two different segments of 5RL,including 79 to 5RL-1 and 6 to 5RL-2,of them 6 were co-localized with the hairy peduncle gene of rye. |
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