Construction of the First SNP-Based Linkage Map Using Genotyping-by-Sequencing and Mapping of the Male-Sterility Gene in Leaf Chicory

Palumbo, Fabio; Qi, Peng; Pinto, Vitor Batista; Devos, Katrien M.; Barcaccia, Gianni

doi:10.3389/fpls.2019.00276

Cited by 17 publications

(34 citation statements)

References 44 publications

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“…The selection was performed taking into consideration chromosomal position, nucleotide length, and repetitive motifs. SSR-specific primer pairs were designed using the Geneious plug-in Primer3 ( Untergasser et al, 2012 ) following the same criteria described by Palumbo et al ( Palumbo et al, 2019a ) and using the same parameters for all genomic loci to make multiplex PCR assays possible.…”

Section: Characterization Of Microsatellites In the Cannabis Genommentioning

confidence: 99%

Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

et al. 2020

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Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and industrial usages. Given the importance of this species, we deepened some of the main challenges-along with potential solutions-behind the breeding of new cannabis cultivars. One of the main issues that should be fixed before starting new breeding programs is the uncertain taxonomic classification of the two main taxa (e.g., indica and sativa) of the Cannabis genus. We tried therefore to examine this topic from a molecular perspective through the use of DNA barcoding. Our findings seem to support a unique species system (C. sativa) based on two subspecies: C. sativa subsp. sativa and C. sativa subsp. indica. The second key issue in a breeding program is related to the dioecy behavior of this species and to the comprehension of those molecular mechanisms underlying flower development, the main cannabis product. Given the role of MADS box genes in flower identity, we analyzed and reorganized all the genomic and transcriptomic data available for homeotic genes, trying to decipher the applicability of the ABCDE model in Cannabis. Finally, reviewing the limits of the conventional breeding methods traditionally applied for developing new varieties, we proposed a new breeding scheme for the constitution of F 1 hybrids, without ignoring the indisputable contribution offered by genomics. In this sense, in parallel, we resumed the main advances in the genomic field of this species and, ascertained the lack of a robust set of SNP markers, provided a discriminant and polymorphic panel of SSR markers as a valuable tool for future marker assisted breeding programs.

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Section: Characterization Of Microsatellites In the Cannabis Genommentioning

confidence: 99%

Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

et al. 2020

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“…Over the last decade, mutation breeding and molecular assisted selection have been further developed with the application of new technologies, especially those related to molecular markers, including restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP) analyses. Collectively, these techniques help to efficiently identify and isolate functional sequences with the goal of improving the precision of breeding [6][7][8][9] . As described by Lander in 1996 10 , SNPs exhibit a typical mutation rate of~10 −9 per nucleotide and have received increasing attention from researchers for their critical role in allele mining, genetic mapping and germplasm identification.…”

Section: Introductionmentioning

confidence: 99%

Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants

Jiang

Liu

et al. 2020

Hortic Res

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Catechins are the predominant products in tea plants and have essential functions for both plants and humans. Several genes encoding the enzymes regulating catechin biosynthesis have been identified, and the identification of single nucleotide polymorphisms (SNPs) resulting in nonsynonymous mutations within these genes can be used to establish a functional link to catechin content. Therefore, the transcriptomes of two parents and four filial offspring were sequenced using next-generation sequencing technology and aligned to the reference genome to enable SNP mining. Subsequently, 176 tea plant accessions were genotyped based on candidate SNPs using kompetitive allelespecific polymerase chain reaction (KASP). The catechin contents of these samples were characterized by highperformance liquid chromatography (HPLC), and analysis of variance (ANOVA) was subsequently performed to determine the relationship between genotypes and catechin content. As a result of these efforts, a SNP within the chalcone synthase (CHS) gene was shown to be functionally associated with catechin content. Furthermore, the geographical and interspecific distribution of this SNP was investigated. Collectively, these results will contribute to the early evaluation of tea plants and serve as a rapid tool for accelerating targeted efforts in tea breeding.

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“…Construction of linkage map by using molecular markers is a crucial step in genetic and genomic analysis that facilitates the discovery of quantitative trait locus/ loci (QTLs) and provides chromosomal information for gene cloning and marker-assisted breeding (Meng et al 2015;Palumbo et al 2019). Since the publication of the first rice linkage map, which included 135 restriction fragment length polymorphism (RFLP) markers (McCouch et al 1988), great progresses have been made in rice linkage map construction, especially with the development of high-throughput sequencing technology in recent years.…”

Section: Introductionmentioning

confidence: 99%

Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

Qu¹,

Shi²,

Chen

et al. 2020

Rice

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Background: The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice. Results: We constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis. Conclusions: In this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.

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Construction of the First SNP-Based Linkage Map Using Genotyping-by-Sequencing and Mapping of the Male-Sterility Gene in Leaf Chicory

Cited by 17 publications

References 44 publications

Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants

Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

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