QTL Mapping of Fruit and Seed-related Traits in Watermelon Using Genotyping-by-Sequencing-based High-density Linkage Mapping

Abstract BackgroundWatermelon is an important vegetable crop with dual use of both fruit and seeds. Understanding the genetic basis of fruit quality and seed size-related traits is important for efficient marker-assisted breeding in watermelon. Linkage mapping in watermelon segregating populations using genotyping-by-sequencing (GBS) provides insights into genetic control of fruit- and seed-related traits and genome collinearity in commercial watermelon cultivars. ResultsIn the present study, we conducted QTL mapping of 12 horticulturally important traits on external and internal fruit quality and seed size/weight using segregating populations derived a cross between two commercial varieties. A high-density genetic map was developed with GBS which contained more than 6,000 SNP loci in 1,004 bins with a total map length of 1261.1 cM and average marker interval of 1.26 cM or 329 kb. Phenotypic data of fruit rind color (RC), rind stripe pattern (RSP), flesh color (FFC), fruit diameter (FD), fruit length (FL), fruit shape index (FSI), fruit weight (FW), Brix content central (BCC), Brix content edge (BCE), seed length (SL), width (SW), and weight (20SWT) were collected from two locations in two years. QTL analysis identified 47 QTL for the 12 traits, of which 24 had moderate- or major-effects, and 34 were novel QTL not identified in previous studies. The QTL for RSP were identified overlapped with previous reports, and mapped the QTL to a small interval on chromosome 6. From the detected novel QTL, we identify FD (qfd2.1), FL (qfl2.1) co-located with FSI (qfsi2.1) QTL on chromosome 2, and the minor QTL qfw3.2 co-located with previously reported fruit shape QTL (qfd3.1, qfl3.1, qfsi3.1), and SW (qsw10.1) co-located with 20SWT QTL (q20swt10.1) on chromosome 10, and 5 minor QTL (qbcc2.1, qbcc5.1, qbce2.1, qbce2.2, qbce5.1) were found to be likely new locus for Brix content.ConclusionWe conducted GBS consisting of 120 F2 individuals and developed a high-density linkage map with more than 6,000 SNP loci in 1004 bins in watermelon. We identified 47 QTL for 12 fruit and seed related traits including 34 novel QTL. Our work expands the molecular breeding toolbox for watermelon to improve the yield and fruit quality.

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High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes

Frontiers in Plant Science ◽

10.3389/fpls.2020.00448 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 2

Author(s):

Mulatu Geleta ◽

Cecilia Gustafsson ◽

Jeffrey C. Glaubitz ◽

Rodomiro Ortiz

Keyword(s):

Linkage Mapping ◽

Genetic Linkage ◽

Genotyping By Sequencing ◽

High Density ◽

Genetic Linkage Mapping

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Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

BMC Genomics ◽

10.1186/s12864-016-2802-3 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 24

Author(s):

Giovanny Covarrubias-Pazaran ◽

Luis Diaz-Garcia ◽

Brandon Schlautman ◽

Joseph Deutsch ◽

Walter Salazar ◽

...

Keyword(s):

Linkage Mapping ◽

Genomic Structure ◽

Genotyping By Sequencing ◽

High Density ◽

American Cranberry

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Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

Scientific Reports ◽

10.1038/s41598-017-01537-2 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 27

Author(s):

Rachit K. Saxena ◽

Vikas K. Singh ◽

Sandip M. Kale ◽

Revathi Tathineni ◽

Swathi Parupalli ◽

...

Keyword(s):

Qtl Mapping ◽

Fusarium Wilt ◽

Genotyping By Sequencing ◽

High Density ◽

Genetic Maps ◽

Wilt Resistance ◽

Fusarium Wilt Resistance

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QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map

BMC Plant Biology ◽

10.1186/s12870-018-1537-5 ◽

2018 ◽

Vol 18 (1) ◽

Cited By ~ 21

Author(s):

L. Pereira ◽

V. Ruggieri ◽

S. Pérez ◽

K. G. Alexiou ◽

M. Fernández ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Map ◽

Fruit Quality ◽

High Density ◽

Quality Traits ◽

Fruit Quality Traits ◽

Melon Fruit

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Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

G3 Genes|Genome|Genetics ◽

10.1534/g3.116.037556 ◽

2017 ◽

Vol 7 (4) ◽

pp. 1177-1189 ◽

Cited By ~ 15

Author(s):

Brandon Schlautman ◽

Giovanny Covarrubias-Pazaran ◽

Luis Diaz-Garcia ◽

Massimo Iorizzo ◽

James Polashock ◽

...

Keyword(s):

Linkage Mapping ◽

Genotyping By Sequencing ◽

High Density ◽

Vaccinium Macrocarpon ◽

American Cranberry

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Construction of a High Density Genetic Map and QTL Mapping of PEG-Induced Drought Tolerance at Seedling Stage in Sesame Using Whole Genome Re-Sequencing

10.21203/rs.3.rs-50720/v1 ◽

2020 ◽

Author(s):

Junchao Liang ◽

Yanying Ye ◽

Xiaowen Yan ◽

Tingxian Yan ◽

Yueliang Rao ◽

...

Keyword(s):

Drought Tolerance ◽

Qtl Mapping ◽

Genetic Map ◽

Phenotypic Variation ◽

Root Length ◽

High Density ◽

Seedling Stage ◽

Whole Genome ◽

Phenotypic Data ◽

Ril Population

Abstract BackgroundImprovement in sesame (Sesamum indicum L.) drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. So far, very few studies have been reported to reveal gene/ quantitative trait loci (QTL) controlling drought tolerance in sesame. To identify the genomic regions associated with drought tolerance, we constructed a high-density genetic map using a recombinant inbred line (RIL) population through whole genome re-sequencing (WGRS) technique. QTLs contributing to three seedling traits were identified under both non-stress and water stress conditions.ResultsThree drought tolerance related traits and their relative values (the ratio of value under stress to value under control condition), including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and PEG-induced osmotic conditions at seedling stage in a RIL population derived from cross of Zhushanbai (ZSB) and Jinhuangma (JHM). Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through WGRS strategy. Composite interval mapping analysis was performed for all the traits as well as their relative phenotypic data. A total of 34 QTLs were detected for these three traits under both conditions and their relative values, and 13 stable QTLs associated with seven traits could be revealed in two independent experiments, explaining on average, 4.95-16.26% of phenotypic variation for each QTL. Four of them contributed more than 10% of phenotypic variation. Root length related QTLs were first identified in sesame. One region on chromosome 12 contained two major QTLs related to RL under osmotic condition and relative RL. ConclusionThe current study reports the first QTL mapping of drought tolerance related traits through a RIL population and first QTL detection of root related trait (root length) in sesame. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

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A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)

BMC Plant Biology ◽

10.1186/s12870-019-2172-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Hua Du ◽

Haiyang Zhang ◽

Libin Wei ◽

Chun Li ◽

Yinghui Duan ◽

...

Keyword(s):

Qtl Mapping ◽

Seed Size ◽

Genetic Map ◽

Seed Coat ◽

Coat Color ◽

Sesamum Indicum ◽

High Density ◽

Oilseed Crop ◽

Seed Coat Color ◽

Specific Length

Abstract Background Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. Results The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. Conclusions This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.

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Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

Scientific Reports ◽

10.1038/s41598-017-16006-z ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 44

Author(s):

Waseem Hussain ◽

P. Stephen. Baenziger ◽

Vikas Belamkar ◽

Mary J. Guttieri ◽

Jorge P. Venegas ◽

...

Keyword(s):

Qtl Mapping ◽

Linkage Map ◽

Bread Wheat ◽

Flag Leaf ◽

Genotyping By Sequencing ◽

Leaf Traits ◽

High Density ◽

High Density Linkage Map

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QTL Mapping for Pumpkin Fruit Traits Using a GBS-based High-density Genetic Map

10.21203/rs.3.rs-1142200/v1 ◽

2022 ◽

Author(s):

Xiaoxia Han ◽

Ziyang Min ◽

Minghua Wei ◽

Yongqi Li ◽

Duanhua Wang ◽

...

Keyword(s):

Genetic Map ◽

Genotyping By Sequencing ◽

Shape Index ◽

Pleiotropic Effect ◽

Fruit Shape ◽

Fruit Weight ◽

High Density ◽

Soluble Solids ◽

Significant Qtls ◽

F2 Population

Abstract Pumpkin is a popular vegetable crop and exhibits a broad diversity in fruit shape and size. Fruit-related traits are the decisive factors determining consumer acceptance and market value of pumpkin cultivar. As a result, deciphering the genetic basis of fruit-related traits is of great importance for pumpkin breeding. To address this problem, a F2 population was generated by two Cucurbita moschata inbred lines with contrasting fruit shapes and genotyping-by-sequencing approach were used to construct a high-density genetic map and localize the QTLs underlying the fruit-related traits in this study. The results showed that a high-quality genetic map was constructed for pumpkin, which comprised of 2413 bins and spanned a total length of 2252.10 cM with an average genetic distance of 0.94 cM. A total of 30 significant QTLs with moderate or small effects were identified for 7 fruit-related traits, including fruit length, fruit diameter, fruit shape index, fruit weight, fruit flesh thickness, seed cavity size, and total soluble solids content. Co-locations and close locations were observed between the QTLs underlying different traits, demonstrating that pleiotropic effect plays an important role in genetic control of fruit-related traits. The identified QTLs provide valuable information for further fine mapping of the related genes and pumpkin breeding programs with the aim of improving fruit quality.

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