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

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.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-021-07499-0 ◽

2021 ◽

Vol 22 (1) ◽

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 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.

Download Full-text

Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

10.21203/rs.3.rs-700179/v2 ◽

2021 ◽

Author(s):

Hui Jiang ◽

Gen Pan ◽

Touming Liu ◽

Li Chang ◽

Siqi Huang ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Snp Markers ◽

Diversity Analysis ◽

Whole Genome ◽

Chromosome 2 ◽

Sequencing Data ◽

Single Nucleotide ◽

Genetic Diversity Analysis ◽

Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

Download Full-text

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.

Download Full-text

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.

Download Full-text

Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber

Scientific Reports ◽

10.1038/s41598-021-83313-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yawo Mawunyo Nevame Adedze ◽

Xia Lu ◽

Yingchun Xia ◽

Qiuyue Sun ◽

Chofong G. Nchongboh ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Pcr Amplification ◽

Reference Sequence ◽

Whole Genome ◽

Sequencing Data ◽

Fresh Market ◽

Breeding Lines ◽

Indel Markers ◽

Indel Polymorphisms ◽

Hybrid Seeds

AbstractInsertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.

Download Full-text

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20194824 ◽

2019 ◽

Vol 20 (19) ◽

pp. 4824 ◽

Cited By ~ 2

Author(s):

Sadia Gull ◽

Zulqarnain Haider ◽

Houwen Gu ◽

Rana Ahsan Raza Khan ◽

Jun Miao ◽

...

Keyword(s):

Oryza Sativa L ◽

Genetic Variations ◽

Indel Marker ◽

Yield Enhancement ◽

Group Method ◽

Arithmetic Means ◽

Rice Varieties ◽

Breeding Programs ◽

Grain Sizes ◽

Indel Markers

The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.

Download Full-text

Development and evaluation of InDel markers in cotton based on whole-genome re-sequencing data

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2019.84100 ◽

2019 ◽

Vol 45 (2) ◽

pp. 196

Author(s):

Mi WU ◽

Nian WANG ◽

Chao SHEN ◽

Cong HUANG ◽

Tian-Wang WEN ◽

...

Keyword(s):

Whole Genome ◽

Sequencing Data ◽

Indel Markers

Download Full-text

Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

10.21203/rs.3.rs-700179/v1 ◽

2021 ◽

Author(s):

Hui Jiang ◽

Gen Pan ◽

Touming Liu ◽

Li Chang ◽

Siqi Huang ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Snp Markers ◽

Diversity Analysis ◽

Whole Genome ◽

Chromosome 2 ◽

Sequencing Data ◽

Single Nucleotide ◽

Genetic Diversity Analysis ◽

Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

Download Full-text