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Li M, Tang Z, Qiu L, Wang Y, Tang S, Fu S. Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye (Secale cereale L.) Chromosome 6. J Genet Genomics 2016; 43:209-16. [PMID: 27090607 DOI: 10.1016/j.jgg.2015.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 11/14/2015] [Accepted: 11/21/2015] [Indexed: 01/15/2023]
Abstract
To effectively use elite genes on the long arm of rye chromosome 6 (the 6RL arm) in wheat breeding programs, precise and fast identification of 6RL chromatin in wheat backgrounds is necessary. PCR-based 6RL-specific markers can facilitate the detection of elite genes on 6RL in wheat breeding. However, only a limited number of 6RL-specific markers have been developed. In the present study, 300 new PCR-based 6RL-specific markers were identified using specific length amplified fragment sequencing (SLAF-seq) technology, and were further physically mapped to four regions on the 6RL arm using 6R and 6RL deletion lines. Interestingly, 127 of the 300 markers were physically localized to a region from the site between 2.3 and 2.5 to the telomere, the same region where the powdery mildew resistance gene was mapped. In addition, 95 of the 300 markers exhibit polymorphisms, which can be used to investigate the diversity of rye 6RL arms. The markers developed in this study can be used to identify given segments of 6RL in wheat backgrounds and accelerate the utilization of elite genes on 6RL in wheat breeding.
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Affiliation(s)
- Meng Li
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Zongxiang Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Ling Qiu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Yangyang Wang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuyao Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Shulan Fu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China.
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Gustafson JP, Ma XF, Korzun V, Snape JW. A consensus map of rye integrating mapping data from five mapping populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:793-800. [PMID: 19066841 DOI: 10.1007/s00122-008-0939-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 11/13/2008] [Indexed: 05/02/2023]
Abstract
A consensus map of rye (Secale cereale L.) was constructed using JoinMap 2.0 based on mapping data from five different mapping populations, including 'UC90' x 'E-line', 'P87' x 'P105', 'I(0.1)-line' x 'I(0.1)-line', 'E-line' x 'R-line', and 'Ds2' x 'RxL10'. The integration of the five mapping populations resulted in a 779-cM map containing 501 markers with the number of markers per chromosome ranging from 57 on 1R to 86 on 4R. The linkage sizes ranged from 71.5 cM on 2R to 148.7 cM on 4R. A comparison of the individual maps to the consensus map revealed that the linear locus order was generally in good agreement between the various populations, but the 4R orientations were not consistent among the five individual maps. The 4R short arm and long arm assignments were switched between the two population maps involving the 'E-line' parent and the other three individual maps. Map comparisons also indicated that marker order variations exist among the five individual maps. However, the chromosome 5R showed very little marker order variation among the five maps. The consensus map not only integrated the linkage data from different maps, but also greatly increased the map resolution, thus, facilitating molecular breeding activities involving rye and triticale.
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Affiliation(s)
- J Perry Gustafson
- USDA-ARS, PGRU, 206 Curtis Hall, University of Missouri, Columbia, MO 65211, USA.
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Abstract
Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.Key words: simple sequence repeats, microsatellites, mapping, rye, Secale cereale.
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Wanous MK, Gustafson JP. A genetic map of rye chromosome 1R integrating RFLP and cytogenetic loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:720-726. [PMID: 24169906 DOI: 10.1007/bf00220949] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/1994] [Accepted: 03/07/1995] [Indexed: 06/02/2023]
Abstract
A genetic map of rye, Secale cereale L., chromosome 1R covering 247 cM was constructed utilizing 27 RFLP and four C-band markers, including terminal C-bands. Genetic mapping of C-bands and the centromere, and in situ hybridization of three RFLP clones, allowed for the integration of the genetic and cytological maps. Eight contact points between the genetic and cytological maps revealed variation in the recombination distance to cytological distance ratio ranging between 0.25 and 1.95, a 7.8-fold difference. Recombination was found to be highest in the satellite region of 1RS and lowest in the most distal region of 1RL.
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Affiliation(s)
- M K Wanous
- Division of Biological Sciences, Tucker Hall, University of Missouri, 65211, Columbia, MO, USA
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