Construction of a genetic linkage map and mapping of drought tolerance trait in Indian beveragial tea

Bali, Sapinder; Mamgain, Akshay; Raina, S. N.; Yadava, Satish Kumar; Bhat, Vishnu; Das, Sudripta; Pradhan, Akshay K.; Goel, Shailendra

doi:10.1007/s11032-015-0306-5

Cited by 20 publications

(10 citation statements)

References 60 publications

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“…To compensate the loss of tester sequences, each subtraction round was followed by amplification round of three cycles with tester-specific primer. The subtracted products were cloned and sequenced as per Bali et al (2015).…”

Section: Representational Difference Analysismentioning

confidence: 99%

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Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)

et al. 2018

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Dioecy and the dynamics of its evolution are intensely investigated aspects of plant reproduction. Seabuckthorn (Hippophae rhamnoides ssp. turkestanica) is an alpine shrub growing wild in certain parts of western Himalaya. The previous studies have reported heteromorphic sex chromosomes in the species and yet marker-based studies indicate high similarity between the male and female genomes. Lack of information on sexual system in the species has further complicated the situation. A systematic study was thus undertaken to understand the sexual system in seabuckthorn and to discern the extent of similarity/dissimilarity between the male and female genomes by generating a large number of markers using amplified fragment length polymorphism and representational difference analysis. Floral biology and regular monitoring of species revealed the presence of polygamomonoecious (PGM) plants in most populations at a low percentage (~2-4%). PGM plants showed low pollen production and overall low fertility, suggesting a monoecy-paradioecy pathway at function. The results of the marker study demonstrated that there are limited differences between male and female genomes and these differences were not uniform across the populations in the Leh-Ladakh region, especially when the geographical distance increases. Results also suggest that a dynamic partitioning of genomes is operational between the two genders of seabuckthorn and differences are not homogenized across the populations. Both reproductive biology-based and DNA marker-based studies indicate that genders have separated recently. The present study proposes seabuckthorn as a promising model system to study evolution of dioecy and sex determination.

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Section: Representational Difference Analysismentioning

confidence: 99%

“…AFLP was performed as per Bali et al (2015). The preamplified products were diluted (1/50) and used for selective amplification.…”

Section: Amplified Fragment Length Polymorphismmentioning

confidence: 99%

Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)

et al. 2018

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“…Strong congruence between component maps has led to successful map integration in other studies [46][47][48] . Combining information from all six parental maps and the '741' self map generated sufficiently high level of congruence (ρ = 0.90, p < 0.01) to allow the generation of integrated maps.…”

Section: Advantages Of Multiple Populations For Genetic Linkage Mappingmentioning

confidence: 99%

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Langdon

King

Baten

et al. 2020

Sci Rep

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the proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

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“…Analysis of a large number of alleles in various populations is made possible by association mapping (Pace et al, 2015;Suwarno et al, 2015;Motilal et al, 2016). Other advantages of GWAS compared with traditional linkage mapping (Tan et al, 2016;Bali et al, 2015) include high-resolution and providing a less time-consuming approach for developing the mapping population (Heena et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing (v0.1)"

2020

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An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93-95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P<1.655E-06).This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result.

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Construction of a genetic linkage map and mapping of drought tolerance trait in Indian beveragial tea

Cited by 20 publications

References 60 publications

Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)

Occurrence of subdioecy and scarcity of gender-specific markers reveal an ongoing transition to dioecy in Himalayan seabuckthorn (Hippophae rhamnoides ssp. turkestanica)

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Peer Review #2 of "Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing (v0.1)"

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