scholarly journals Generation of a High-Density Genetic Map of Pepper (Capsicum annuum L.) by SLAF-seq and QTL Analysis of Phytophthora capsici Resistance

Horticulturae ◽  
2021 ◽  
Vol 7 (5) ◽  
pp. 92
Author(s):  
Yi-Fei Li ◽  
Shi-Cai Zhang ◽  
Xiao-Miao Yang ◽  
Chun-Ping Wang ◽  
Qi-Zhong Huang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Capsicum Annuum ◽  
Genetic Map ◽  
Phytophthora Capsici ◽  
Female Parent ◽  
High Density ◽  
Phenotypic Variance ◽  
Capsicum Annuum L ◽  
Reverse Transcription Pcr ◽  
Mapping Panel

Pepper (Capsicum annuum L.) is an economically significant global crop and condiment. Its yield can be severely reduced by the oomycete plant pathogen, Phytophthora capsici (P. capsici). Here, a high-density genetic map was created with a mapping panel of F2 populations obtained from 150 individuals of parental lines PI201234 and 1287 and specific-locus amplified fragment sequencing (SLAF) that was then utilized to identify loci that are related to resistance to P. capsici. The sequencing depth of the genetic map was 108.74-fold for the male parent, 126.25-fold for the female parent, and 22.73-fold for the offspring. A high-resolution genetic map consisting of 5565 markers and 12 linkage groups was generated for pepper, covering 1535.69 cM and an average marker distance of 0.28 cM. One major quantitative trait locus (QTL) for the P. capsici resistance (CQPc5.1) was identified on Chr05 that explained the observed 11.758% phenotypic variance. A total of 23 candidate genes located within the QTL CQPc5.1 interval were identified, which included the candidate gene Capana05g000595 that encodes the RPP8-like protein as well as two candidate genes Capana05g000596 and Capana05g000597 that encodes a RPP13-like protein. Quantitative reverse-transcription PCR (qRT-PCR) revealed higher expression levels of Capana05g000595, Capana05g000596, and Capana05g000597 in P. capsici resistance accessions, suggesting their association with P. capsici resistance in pepper.

scholarly journals High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiao-fen Zhang ◽  
Guo-yun Wang ◽  
Ting-ting Dong ◽  
Bin Chen ◽  
He-shan Du ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Capsicum Annuum ◽  
Genetic Map ◽  
High Density ◽  
Capsicum Annuum L ◽  
Map Construction

Alterations in peroxidase activity and phenylpropanoid metabolism induced by Nacobbus aberrans Thorne and Allen, 1944 in chilli (Capsicum annuum L.) CM334 resistant to Phytophthora capsici Leo.

2010 ◽  
Vol 338 (1-2) ◽  
pp. 399-409 ◽  
Author(s):  
Noé López-Martínez ◽  
Ma. Teresa Colinas-León ◽  
Cecilia B. Peña-Valdivia ◽  
Yolanda Salinas-Moreno ◽  
Patricia Fuentes-Montiel ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Peroxidase Activity ◽  
Phytophthora Capsici ◽  
Phenylpropanoid Metabolism ◽  
Capsicum Annuum L ◽  
Nacobbus Aberrans

scholarly journals Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zemao Yang ◽  
Youxin Yang ◽  
Zhigang Dai ◽  
Dongwei Xie ◽  
Qing Tang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Qtl Mapping ◽  
Genetic Map ◽  
Quantitative Trait ◽  
High Density ◽  
Genetic Maps ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Qtls Mapping

Abstract Background Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. Results We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58–19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. Conclusions We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.

Fine-mapping QTLs and the validation of candidate genes for Aluminum tolerance using a high-density genetic map

2019 ◽  
Vol 444 (1-2) ◽  
pp. 119-137 ◽  
Author(s):  
Zhandong Cai ◽  
Yanbo Cheng ◽  
Peiqi Xian ◽  
Rongbin Lin ◽  
Qiuju Xia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
Fine Mapping ◽  
Aluminum Tolerance ◽  
High Density

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

scholarly journals Phosphite effect on hot and sweet pepper reaction to Phytophthora capsici

2004 ◽  
Vol 61 (5) ◽  
pp. 492-495 ◽  
Author(s):  
Fernando Cesar Sala ◽  
Cyro Paulino da Costa ◽  
Márcia de Moraes Echer ◽  
Marise Cagnin Martins ◽  
Sally Ferreira Blat
Keyword(s):  
Capsicum Annuum ◽  
Plant Resistance ◽  
Adult Stage ◽  
Phytophthora Capsici ◽  
Sweet Pepper ◽  
Hot Pepper ◽  
Heterozygous Genotype ◽  
Capsicum Annuum L ◽  
Fruiting Stage ◽  
Resistant Lines

Phosphite has been recommended to enhance plant resistance against Phytophthora. This work evaluated the response of hot and sweet pepper (Capsicum annuum L.) to Phytophthora capsici from juvenile up to the adult stage following treatment with phosphite. Sweet pepper hybrids considered to be resistant to P. capsici, like Reinger, Nathalie and Athenas, were evaluated. The susceptible checks were hybrid Magali R and cvs. Myr 10 and Ikeda. Hot pepper Criollo de Morelos 328, CM 334, BGH 3756, BGH 5122, CNPH 294 and Locorte were used as referential resistant lines. Phosphite did not have an effect on the hot pepper resistant lines because of their genetic homozygozity, while no protection was observed for the Athenas hybrid claimed to be resistant. Heterozygous hybrids recognized as resistant, like Reinger and Nathalie, showed higher survival following phosphite treatment, and their reaction was equivalent to the resistant cvs. CM 328 and CM 334, except for the fruiting stage. Depending of the hybrid heterozygous genotype, phosphite possibly acts through indirect phytoalexin induction through the inhibited pathogen.

scholarly journals Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number

2020 ◽  
Vol 11 ◽  
Author(s):  
Qiao Li ◽  
Zhifen Pan ◽  
Yuan Gao ◽  
Tao Li ◽  
Junjun Liang ◽  
...  
Keyword(s):  
Genetic Map ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
High Density ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Quality Traits ◽  
Rna Seq ◽  
Falling Number ◽  
7S Globulin

Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31–47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58–25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.

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