Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population

Maheswaran, M.; Subudhi, Prasanta K.; Nandi, Sukdeb; Xu, Jintao; Parco, Arnold; Yang, Daichang; Huang, Ning

doi:10.1007/s001220050379

Cited by 135 publications

(84 citation statements)

References 15 publications

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“…The key difference is that in ALFP, the fragments are then size-separated using polyacrylamide gel electrophoresis (PAGE) as a means of identifying size variants while GBS uses next-gen sequencing to identify SNP variants (Vos et al 1995). Two different groups working with an IR64xAzucena double haploid population (developed using the same IR64xAzucena parents as in this RIL population) noted that chromosomes were "stretched" with the integration of AFLP markers into RFLP genetic maps (Maheswaran et al 1997;Virk et al 1998). In 1996 specifically noted a correlation between genetic map size and the number of AFLP markers and hypothesized that these expansions had to be the result of map function error, possibly as a result of segregation distortion (Maheswaran et al 1997).…”

Section: Discussionmentioning

confidence: 99%

“…Two different groups working with an IR64xAzucena double haploid population (developed using the same IR64xAzucena parents as in this RIL population) noted that chromosomes were "stretched" with the integration of AFLP markers into RFLP genetic maps (Maheswaran et al 1997;Virk et al 1998). In 1996 specifically noted a correlation between genetic map size and the number of AFLP markers and hypothesized that these expansions had to be the result of map function error, possibly as a result of segregation distortion (Maheswaran et al 1997). Virk et al, followed up on this hypothesis in 1997 by trying to reduce the size of their genetic map by controlling for segregation distortion, without success (Virk et al 1998).…”

Section: Discussionmentioning

confidence: 99%

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Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

et al. 2013

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Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) x japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparcity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has great value for numerous applications in rice breeding and genetics research.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

et al. 2013

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“…Amplified fragment length polymorphism (AFLP) (Vos et al, 1995) depends on the reliability of restriction fragment length polymorphism and the high efficiency of polymerase chain reaction (PCR) to amplify digested genome DNA segments selectively. AFLP is highly reliable for the assessment of genetic variation among and within populations (Maheswaran et al, 1997). AFLP has been widely applied to study genotyping, population differentiation, and genetic diversity in a wide variety of organisms, such as catfish (Mickett et al, 2003), tilapia (Agrestia et al, 2000), and penaeid shrimp (Wang et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity among red swamp crayfish (Procambarus clarkii) populations in the middle and lower reaches of the Yangtze River based on AFLP markers

Zhu¹,

Huang²,

Dai³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. The red swamp crayfish has become one of the most important freshwater aquaculture species in China. At present, although it is widely distributed in the middle and lower reaches of the Yangze River basin, little is known about its population genetics and geographic distribution in China. We estimated the genetic diversity among 6 crayfish populations from 4 lakes (Hongze Lake, Poyang Lake, Dongting Lake, and Yue Lake) using AFLPs. A total of 129 loci were generated with 5 EcoRI-MseI primer combinations and scored as binary data in 139 individuals. These data were analyzed by cluster methods with the NTSYSpc software package. The 6 populations were separated into 3 major clusters by principal coordinate analysis and cluster analysis. Among the 6 populations, the highest gene diversity was found within the Nanjing population. Analysis of molecular variance demonstrated that most variation occurred within populations (91.20%). The estimated average G ST value across all loci was 0.4186, suggesting (very) low gene flow among the different localities. We conclude that there is high genetic differentiation among crayfish in the middle and lower reaches of the Yangze River. This information will help in the selection of highquality individuals for artificial reproduction.

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“…For instance, 70 AFLP markers specific to the donor G. sturtianum were detected, while the RAPD study revealed only 49 G. sturtianum-specific markers . AFLP is therefore a powerful technique for DNA fingerprinting in cotton, as demonstrated in other crops (Maheswaran et al 1997;VanToai et al 1997;Paran et al 1998). Although the similarity of some BC progenies at the DNA level with cultivated cotton increased with backcrossing and selfing, some other progenies expressed a similarity lower than that observed between their mother parent and the upland cotton G. hirsutum.…”

Section: Discussionmentioning

confidence: 99%

Breeding for ”low-gossypol seed and high-gossypol plants” in upland cotton. Analysis of tri-species hybrids and backcross progenies using AFLPs and mapped RFLPs

Bi¹,

Maquet²,

Baudoin³

et al. 1999

Theor Appl Genet

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This work aims at breeding upland cotton [Gossypium hirsutum L., 2(AD) 1 genome] with a reduced level of gossypol in the seeds for optimal food and feed uses, and a high gossypol level in the remaining organs for resistance to pests. Two tri-species Gossypium hybrids, (G. thurberi-G. sturtianum-G. hirsutum and G. hirsutum-G. raimondii-G. sturtianum) including G. sturtianum (2C 1 ) as a donor, G. thurberi (2D 1 ) and G. raimondii (2D 5 ) as a bridge species, were created. Recurrent selection initiated with these tri-species hybrids produced backcross (BC) progenies expressing the "lowgossypol seed and high-gossypol plant" trait at different levels. We used AFLP markers to assess the genetic similarity among the germplasm and RFLP probes to tag the introgression of specific chomosome segments from the parental species. Five pairs of AFLP primers generated 477 fragments, among which 417 (87.4%) were polymorphic. The genetic similarity between the upland cotton and the wild species ranged from 29.5 to 43.2%, while similarity reached 80% between upland cotton and BC3 plants. Introgression of species-specific AFLPs was evident from all the parental species and confirmed the hybrid origin of the analyzed progenies. Southern-blot analysis based on 49 RFLP probes allowed us to trace the introgression of parental DNA segments in the trispecies hybrids and in three generations of backcross. Introgression was evident from 11, 8 and 7 linkage groups of G. sturtianum, G. raimondii and G. thurberi respectively. The types of introgression revealed by RFLP probes are discussed, and breeding schemes to enhance recombination are proposed. The ability to trace DNA segments of known chromosomal locations from the donor G. sturtianum through segregating generations is a starting point to map the "low-gossypol seed and highgossypol plant" traits.

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Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population

Cited by 135 publications

References 15 publications

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

Genetic diversity among red swamp crayfish (Procambarus clarkii) populations in the middle and lower reaches of the Yangtze River based on AFLP markers

Breeding for ”low-gossypol seed and high-gossypol plants” in upland cotton. Analysis of tri-species hybrids and backcross progenies using AFLPs and mapped RFLPs

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