Sikandar Amanullah1,2, Benjamin Agyei Osae1,2, Tiantian Yang1,2, Farhat Abbas3, Shi Liu1,2, Hongyu Liu1,2, Xuezheng Wang1,2, Peng Gao4,5, Feishi Luan6,7. 1. College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China. 2. Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China. 3. College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, People's Republic of China. 4. College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China. gaopeng_neau@163.com. 5. Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China. gaopeng_neau@163.com. 6. College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin, 150030, People's Republic of China. luanfeishi@neau.edu.cn. 7. Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China. luanfeishi@neau.edu.cn.
Abstract
BACKGROUND: Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding. METHODS AND RESULTS: In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-F2 derived plant populations were genotyped for linkage mapping and composite interval mapping based QTL mapping exposed 6 genetic loci, positioned over distinct chromosomes (02, 04, 08, 09, and 12) between the flanking intervals of CAPS markers, which explained an unlinked polygenic architecture in genome. Three minor QTLs of fruit weight (FWt2.1, FWt4.1, FWt9.1), one major QTL of fruit firmness (FrFir8.1), one major QTL of fruit length (FL12.1), and one major QTL of fruit shape (FS12.1) were determined and collectively explained the phenotypic variance from 5.64 to 15.64%. Fruit phenotypic correlation exhibited the significant relationship and principal component analysis also identified the potential variability. Multiple sequence alignments also indicated the significant base-mutations in the detected genetic loci, respectively. CONCLUSION: In short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.
BACKGROUND: Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding. METHODS AND RESULTS: In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-F2 derived plant populations were genotyped for linkage mapping and composite interval mapping based QTL mapping exposed 6 genetic loci, positioned over distinct chromosomes (02, 04, 08, 09, and 12) between the flanking intervals of CAPS markers, which explained an unlinked polygenic architecture in genome. Three minor QTLs of fruit weight (FWt2.1, FWt4.1, FWt9.1), one major QTL of fruit firmness (FrFir8.1), one major QTL of fruit length (FL12.1), and one major QTL of fruit shape (FS12.1) were determined and collectively explained the phenotypic variance from 5.64 to 15.64%. Fruit phenotypic correlation exhibited the significant relationship and principal component analysis also identified the potential variability. Multiple sequence alignments also indicated the significant base-mutations in the detected genetic loci, respectively. CONCLUSION: In short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.
Authors: C. Périn; S. Hagen; V. De Conto; N. Katzir; Y. Danin-Poleg; V. Portnoy; S. Baudracco-Arnas; J. Chadoeuf; C. Dogimont; M. Pitrat Journal: Theor Appl Genet Date: 2002-03-27 Impact factor: 5.699
Authors: Eduard Moreno; Javier M Obando; Noelia Dos-Santos; J Pablo Fernández-Trujillo; Antonio J Monforte; Jordi Garcia-Mas Journal: Theor Appl Genet Date: 2007-12-20 Impact factor: 5.699
Authors: Mohamed Zarid; Victor García-Carpintero; Cristina Esteras; Juan Esteva; María C Bueso; Joaquín Cañizares; María B Picó; Antonio J Monforte; J Pablo Fernández-Trujillo Journal: J Sci Food Agric Date: 2020-09-09 Impact factor: 3.638
Authors: Aurora Díaz; Ana Montserrat Martín-Hernández; Ramón Dolcet-Sanjuan; Ana Garcés-Claver; José María Álvarez; Jordi Garcia-Mas; Belén Picó; Antonio José Monforte Journal: Theor Appl Genet Date: 2017-06-05 Impact factor: 5.699
Authors: Aurora Diaz; Mohamed Fergany; Gelsomina Formisano; Peio Ziarsolo; José Blanca; Zhanjun Fei; Jack E Staub; Juan E Zalapa; Hugo E Cuevas; Gayle Dace; Marc Oliver; Nathalie Boissot; Catherine Dogimont; Michel Pitrat; René Hofstede; Paul van Koert; Rotem Harel-Beja; Galil Tzuri; Vitaly Portnoy; Shahar Cohen; Arthur Schaffer; Nurit Katzir; Yong Xu; Haiying Zhang; Nobuko Fukino; Satoru Matsumoto; Jordi Garcia-Mas; Antonio J Monforte Journal: BMC Plant Biol Date: 2011-07-28 Impact factor: 4.215
Authors: Padma Nimmakayala; Yan R Tomason; Venkata L Abburi; Alejandra Alvarado; Thangasamy Saminathan; Venkata G Vajja; Germania Salazar; Girish K Panicker; Amnon Levi; William P Wechter; James D McCreight; Abraham B Korol; Yefim Ronin; Jordi Garcia-Mas; Umesh K Reddy Journal: Front Plant Sci Date: 2016-09-22 Impact factor: 5.753