High-Density GBS-Based Genetic Linkage Map Construction and QTL Identification Associated With Yellow Mosaic Disease Resistance in Bitter Gourd (Momordica charantia L.)

Yellow mosaic disease (YMD) in bitter gourd (Momordica charantia) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent “Punjab-14” and the resistant parent “PAUBG-6” were crossed to obtain F4 mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1, qYMD.pau_4.1, and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1, qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.

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A genetic linkage map of allo-octoploid strawberry (Fragaria × ananassa Duch.) using SNP markers

Korean Journal of Breeding Science ◽

10.9787/kjbs.2017.49.3.119 ◽

2017 ◽

Vol 49 (3) ◽

pp. 119-128 ◽

Cited By ~ 4

Author(s):

Ye Rin Lee ◽

Jundae Lee

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Snp Markers ◽

Fragaria Ananassa

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Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated QTLs

Trees ◽

10.1007/s00468-014-1090-2 ◽

2014 ◽

Vol 28 (6) ◽

pp. 1823-1835 ◽

Cited By ~ 10

Author(s):

P. Moraga-Suazo ◽

L. Orellana ◽

P. Quiroga ◽

C. Balocchi ◽

E. Sanfuentes ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

Pinus Radiata ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Pitch Canker ◽

Canker Disease

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A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

Plant Genetics Genomics and Biotechnology ◽

10.5147/pggb.v1i3.154 ◽

2017 ◽

Vol 1 (3) ◽

pp. 80-89 ◽

Cited By ~ 2

Author(s):

Masum Akond ◽

Shiming Liu ◽

Lauren Schoener ◽

James A. Anderson ◽

Stella K. Kantartzi ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Goodness Of Fit ◽

Genetic Linkage Map ◽

Agronomic Traits ◽

Snp Markers ◽

High Density ◽

Genotyping Array ◽

Glycine Max L ◽

Average Marker Density

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.

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Construction of a genetic linkage map in Fenneropenaeus chinensis using SNP markers

Russian Journal of Marine Biology ◽

10.1134/s1063074013020107 ◽

2013 ◽

Vol 39 (2) ◽

pp. 136-142 ◽

Cited By ~ 4

Author(s):

Jian-Yong Zhang ◽

Wei-Ji Wang ◽

Jie Kong ◽

Qing-Yin Wang

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Fenneropenaeus Chinensis ◽

Snp Markers

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The first genetic linkage map of Primulina eburnea (Gesneriaceae) based on EST-derived SNP markers

Journal of Genetics ◽

10.1007/s12041-016-0650-1 ◽

2016 ◽

Vol 95 (2) ◽

pp. 377-382 ◽

Cited By ~ 1

Author(s):

CHEN FENG ◽

CHAO FENG ◽

MING KANG

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Snp Markers

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A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

Journal of Integrative Agriculture ◽

10.1016/s2095-3119(14)60902-3 ◽

2015 ◽

Vol 14 (9) ◽

pp. 1697-1705 ◽

Cited By ~ 5

Author(s):

Hui-jie ZHAI ◽

Zhi-yu FENG ◽

Xin-ye LIU ◽

Xue-jiao CHENG ◽

Hui-ru PENG ◽

...

Keyword(s):

Triticum Aestivum ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Triticum Aestivum L ◽

Snp Markers ◽

Ril Population

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An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology

Agronomy ◽

10.3390/agronomy10010114 ◽

2020 ◽

Vol 10 (1) ◽

pp. 114 ◽

Cited By ~ 2

Author(s):

Xiaoxia Yu ◽

Mingfei Zhang ◽

Zhuo Yu ◽

Dongsheng Yang ◽

Jingwei Li ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Large Scale ◽

High Throughput Sequencing ◽

Genetic Linkage Map ◽

De Novo ◽

Snp Markers ◽

High Density ◽

Tetraploid Potato ◽

Specific Length

Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.

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QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine

10.21203/rs.3.rs-49639/v2 ◽

2020 ◽

Author(s):

dawei Wang ◽

chen Shi ◽

Siguang Li ◽

Hongyan Tang ◽

Chenzhong He ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Phenotypic Variance ◽

Basal Diameter ◽

Exploitation And Utilization ◽

Information Construction ◽

Genomic Studies ◽

Needle Diameter

Abstract Background: Simao pine is one of the primary economic tree species for resin and timber production in southwest China. The exploitation and utilization of Simao pine are constrained by the relatively lacking of genetic information. Construction a fine genetic linkage map and detecting quantitative trait locis (QTLs) for growth-related traits is a prerequisite section of Simao Pine's molecular breeding program. Results: In our study, a high-resolution Simao pine genetic map employed specific locus amplified fragment sequencing (SLAF-seq) technology and based on an F1 pseudo-testcross population has been constructed. There were 11,544 SNPs assigned to 12 linkage groups (LGs), and the total length of the map was 2,062.85 cM with a mean distance of 0.37 cM between markers. According to the phenotypic variation analysis for three consecutive years, a total of seventeen QTLs for four traits were detected. Among 17 QTLs, there were six for plant height (Dh.16.1, Dh16.2, Dh17.1, Dh18.1-3), five for basal diameter (Dbd.17.1-5), four for needle length (Dnl17.1-3, Dnl18.1) and two for needle diameter (Dnd17.1 and Dnd18.1) respectively. These QTLs individually explained phenotypic variance from 11.0-16.3 %, and the logarithm of odds (LOD) value ranged from 2.52 to 3.87. Conclusions: In our study, a fine genetic map of Simao pine applied the technology of SLAF-seq has been constructed for the first time. Based on the map, a total of 17 QTLs for four growth-related traits were identified. It provides helpful information for genomic studies and marker-assisted selection (MAS) in Simao pine.

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