Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

Xu, Youqiang; Zhu, Lihuang; Xiao, Jin‐Hua; Huang, Ning; McCouch, Susan R.

doi:10.1007/s004380050355

Cited by 381 publications

(287 citation statements)

References 89 publications

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“…By saturating the population with 30,984 SNPs, we were able to define regions of segregation distortion down to .24 Mb --the recombinational limits in an RIL population of this kind, thus identifying regions of candidate sterility genes. The majority of these regions, including those on chromosomes 1, 3, 4, 6, 8, and 11, correspond to previously identified putative sterility loci, lending further validation to the value of our dataset for both mapping segregation distortion and identifying putative sterility loci (Harushima et al 2001;Harushima et al 2002;Wu et al 2010;Xu et al 1997;Garavito et al 2010;Matsubara et al 2011). …”

Section: Discussionsupporting

confidence: 79%

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: Discussionsupporting

confidence: 79%

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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“…Of all the markers tested, DNA marker like SSR is widely adopted due to its codominant nature and abundant in rice genome. In the present study, out of forty polymorphic markers, 9 (22.5%) showed skewed segregation in DH population derived from anthers of CRHR32 which is found lower as compared to the DHs derived from indica-japonica inter-crossing (41%) (Huang et al 1997). The presence of segregation distortion factors like hybrid sterility (S) genes and gametophyte competition (ga) genes are often associated with the segregation distortion in rice (Nakagahra 1972;Sano 1990).…”

Section: Discussionmentioning

confidence: 61%

Doubled Haploids generated through anther culture from an elite long duration rice hybrid, CRHR32: Method optimization and molecular characterization

Rout

Naik

Ngangkham

et al. 2016

Plant Biotechnology

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An improved procedure has been developed for high frequency androgenesis in an elite long duration indica rice hybrid. The effects of cold temperature pretreatment, duration of treatment and media with different plant growth regulators on callus induction and shoot regeneration were examined for generation of doubled haploids. N6 medium supplemented with 2.0 mg l −1 2,4-D, 0.5 mg l −1 BAP and 30 g l −1 maltose was found to be most effective for callusing when compared with MS and SK1. The N6 media grown calli showed maximum green shoot regeneration frequency in MS medium supplemented with 0.5 mg l −1 NAA, 0.5 mg l −1 Kinetin, 1.5 mg l −1 BAP and 30 g l −1 sucrose after 2 week of culture. The cold temperature treatment of spike at 10°C for 2 days alongside by 8 days was found to be most suitable conditions for callusing and green shoot regeneration producing 186 green plants from indica rice hybrid, CRHR32. The ploidy status assessed on the basis of morpho-agronomic characters revealed fertile diploids at a frequency of about 81.10%; 16.10%, 2.68% and 1.08% were polyploids, haploids and mixploids respectively. Microsatellite marker analysis showed 1 : 1 ratio of the alleles of CMS and restorer lines used for development of CRHR32. Homozygosity was detected for all the marker loci in 150 DHs and only one plant was identified as heterozygote. This investigation identified the favorable media composition and condition for callus induction and green plant regeneration which would further increase the knowledge and better understanding in rice hybrids for development of DHs.

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“…The SD system was found first in Drosophila and has been studied extensively (Lyttle 1991). It has also been found in many plant species, including rice (Xu et al 1997), wheat (Farisa et al 1998), maize (Lu et al 2002), barley (Kleinhofs et al 1993), and coffee (Ky et al 2000). In our high-density SSR map, only two regions on the nine major LGs showed significant segregation distortion.…”

Section: Suppression Of Recombination In the Msymentioning

confidence: 81%

Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales

Chen

Hou

et al. 2007

Genetics

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A high-density genetic map of papaya (Carica papaya L.) was constructed using microsatellite markers derived from BAC end sequences and whole-genome shot gun sequences. Fifty-four F 2 plants derived from varieties AU9 and SunUp were used for linkage mapping. A total of 707 markers, including 706 microsatellite loci and the morphological marker fruit flesh color, were mapped into nine major and three minor linkage groups. The resulting map spanned 1069.9 cM with an average distance of 1.5 cM between adjacent markers. This sequence-based microsatellite map resolved the very large linkage group 2 (LG 2) of the previous high-density map using amplified fragment length polymorphism markers. The nine major LGs of our map represent papaya's haploid nine chromosomes with LG 1 of the sex chromosome being the largest. This map validates the suppression of recombination at the male-specific region of the Y chromosome (MSY) mapped on LG 1 and at potential centromeric regions of other LGs. Segregation distortion was detected in a large region on LG 1 surrounding the MSY region due to the abortion of the YY genotype and in a region of LG6 due to an unknown cause. This high-density sequencetagged genetic map is being used to integrate genetic and physical maps and to assign genome sequence scaffolds to papaya chromosomes. It provides a framework for comparative structural and evolutional genomic research in the order Brassicales. Papaya is a perennial plant species that flowers as early as 3 months and produces fruit in 9 months; it is trioecious with an intriguing sex determination system with three basic sex types: male, female, and hermaphrodite. A high-density genetic map of papaya, constructed using 1498 AFLP and three morphological markers revealed severe suppression of recombination at the sex determination locus with 225 cosegregating markers accounting for 66% of the markers on linkage group 1 (LG 1) and 15% of the markers genomewide . This AFLP map provided a critical piece of evidence for defining the primitive Y chromosome in papaya . Sequence comparison of Y-specific fragments from males and hermaphrodites confirmed that 1

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Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

Cited by 381 publications

References 89 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

Doubled Haploids generated through anther culture from an elite long duration rice hybrid, CRHR32: Method optimization and molecular characterization

Construction of a Sequence-Tagged High-Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales

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