Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)

Abstract Background The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. Conclusions This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

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Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)

10.21203/rs.3.rs-31351/v1 ◽

2020 ◽

Author(s):

Junjie Cui ◽

Jiazhu Peng ◽

Jiaowen Cheng ◽

Kailin Hu

Keyword(s):

Genetic Map ◽

Average Density ◽

Momordica Charantia ◽

Bitter Gourd ◽

Map Construction ◽

Indel Markers ◽

Genome Wide ◽

Indel Polymorphisms ◽

Molecular Marker Development ◽

Development And Validation

Abstract Background: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd ( Momordica charantia ), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1,298 InDels/Mb. Then we developed a total of 2,502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47-2-1-1-3’ and ‘04-17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47-2-1-1-3’×‘04-17’ F 2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. Conclusions: This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

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Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd ( Momordica charantia )

10.21203/rs.3.rs-31351/v2 ◽

2020 ◽

Author(s):

Junjie Cui ◽

Jiazhu Peng ◽

Jiaowen Cheng ◽

Kailin Hu

Keyword(s):

Genetic Map ◽

Average Density ◽

Momordica Charantia ◽

Bitter Gourd ◽

Map Construction ◽

Indel Markers ◽

Genome Wide ◽

Indel Polymorphisms ◽

Molecular Marker Development ◽

Development And Validation

Abstract Background: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1,298 InDels/Mb. Then we developed a total of 2,502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47-2-1-1-3’ and ‘04-17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47-2-1-1-3’×‘04-17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome.Conclusions: This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

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Genome-wide Development of Insertion-deletion (InDel) Markers Database for Cannabis and its uses for Genetic Structure Analysis of Chinese Germplasm and Identification of Sex-linked Marker

10.21203/rs.3.rs-265241/v1 ◽

2021 ◽

Author(s):

Gen Pan ◽

Zheng Li ◽

Siqi Huang ◽

Jie Tao ◽

Yaliang Shi ◽

...

Keyword(s):

Genetic Structure ◽

Cannabis Sativa ◽

Economic Value ◽

Germplasm Conservation ◽

Polymorphism Analysis ◽

Indel Markers ◽

Genome Wide ◽

A Genome ◽

Indel Polymorphisms ◽

Chinese Germplasm

Abstract Background: Cannabis sativa L., a dioecious plant, derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties were usually harnessed depending on the sex of the plant. To analyze the genetic structure of Chinese cannabis and identify sex-linked makers, the genome-wide insertion-deletion (InDel) markers were designed and used. Results: In this study, a genome-wide analysis of insertion–deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47558 InDels were detected between the two varieties, and the length of InDels ranged from 4 bp to 87 bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 had the highest number of InDels among the cannabis chromosomes, while chromosome 10 had the lowest number. Additionally, a total of 47558 InDel markers were designed, and 84 primers evenly distributed in the cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the Indel markers as well as the flowering time, the 115 Chinese germplasms were divided in two subgroups, which were mainly composed of cultivars from the most north and south regions, respectively. Additional, the marker “ I1-10” was found to amplify two bands (398bp and 251bp) in the male plants, while a 389bp bands in female plants. Using this marker, the feminized and dioecious varieties can also be distinguished.Conclusion: This study will facilitate the genetic improvement and germplasm conservation of cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for cannabis breeding and production.

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Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing

Frontiers in Plant Science ◽

10.3389/fpls.2016.00334 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 4

Author(s):

Zhenqing Zhao ◽

Honghui Gu ◽

Xiaoguang Sheng ◽

Huifang Yu ◽

Jiansheng Wang ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Genetic Map ◽

High Density ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Map Construction ◽

Genome Wide ◽

Specific Locus

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Genome-wide development of insertion-deletion (InDel) markers for Cannabis and its uses in genetic structure analysis of Chinese germplasm and sex-linked marker identification

BMC Genomics ◽

10.1186/s12864-021-07883-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gen Pan ◽

Zheng Li ◽

Siqi Huang ◽

Jie Tao ◽

Yaliang Shi ◽

...

Keyword(s):

Genetic Structure ◽

Cannabis Sativa ◽

Economic Value ◽

Germplasm Conservation ◽

Polymorphism Analysis ◽

Indel Markers ◽

Genome Wide ◽

A Genome ◽

Indel Polymorphisms ◽

Chinese Germplasm

Abstract Background Cannabis sativa L., a dioecious plant derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties have been usually harnessed depending on the sex of the plant. To analyse the genetic structure of Chinese Cannabis and identify sex-linked makers, genome-wide insertion-deletion (InDel) markers were designed and used. Results In this study, a genome-wide analysis of insertion-deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47,558 InDels were detected between the two varieties, and the length of InDels ranged from 4 bp to 87 bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 exhibited the highest number of InDels among the Cannabis chromosomes, while chromosome 10 exhibited the lowest number. Additionally, 31,802 non-redundant InDel markers were designed, and 84 primers evenly distributed in the Cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the InDel markers and the flowering time, the 115 Chinese germplasms were divided into two subgroups, mainly composed of cultivars obtained from the northernmost and southernmost regions, respectively. Additional two markers, “Cs-I1–10” and “Cs-I1–15”, were found to amplify two bands (398 bp and 251 bp; 293 bp and 141 bp) in the male plants, while 389-bp or 293-bp bands were amplified in female plants. Using the two markers, the feminized and dioecious varieties could also be distinguished. Conclusion Based on the findings obtained herein, we believe that this study will facilitate the genetic improvement and germplasm conservation of Cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for Cannabis breeding and production.

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Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia)

Frontiers in Plant Science ◽

10.3389/fpls.2017.01103 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 5

Author(s):

Junjie Cui ◽

Jiaowen Cheng ◽

Dingguo Nong ◽

Jiazhu Peng ◽

Yafei Hu ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Momordica Charantia ◽

Bitter Gourd ◽

Genome Wide Analysis ◽

Genome Wide ◽

Simple Sequence

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Development of InDel Markers and Fingerprinting of Bitter Gourd (Momordica Charantia) Based on Whole Genome Re-sequencing

10.21203/rs.3.rs-810603/v1 ◽

2021 ◽

Author(s):

Liwen Su ◽

Lianlian Ma ◽

Xiaochun Huang ◽

Wenting Wu ◽

Haixuan Lv ◽

...

Keyword(s):

Polyacrylamide Gel Electrophoresis ◽

Momordica Charantia ◽

Bitter Gourd ◽

Group Method ◽

Whole Genome ◽

Sequencing Data ◽

African Countries ◽

Arithmetic Means ◽

Relationship Analysis ◽

Indel Markers

Abstract Bitter gourd (Momordica charantia L.) is one of the most important vegetable crops in many Asian and African countries. Here, InDel markers developed by comparing whole genome re-sequencing data were used to analyze the genetic diversity of a bitter gourd germplasm sample from various geographical origins. To verify the reliability of the set of InDel markers identified, 220 pairs of InDel primers were designed. The primers were preliminarily detected by 8% polyacrylamide gel electrophoresis, and 25 pairs of primers with better polymorphism were screened. Using the 25 primer combinations, the 53 bitter gourd accessions were effectively distinguished and the InDel fingerprint of DNA was constructed. Concomitantly, the degree of purity of different crosses was determined based on the differences in specific bands among genotypes. The unweighted pair-group method with arithmetic means showed that the 53 bitter gourd materials may be divided into three groups, with a similarity coefficient of 0.645 as the threshold. Therefore, this study can provide many InDel markers for genotypic identification, genetic relationship analysis, and genetic map construction of bitter gourd.

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