Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line ‘Wongyo 3115’, using long- and short-read sequencing technologies. The assembly of ‘Wongyo 3115’ produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the ‘Wongyo 3115’ reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the ‘BS F2’ populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the ‘Wongyo 3115’ genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of ‘BS F2’ obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

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Chromosome-level genome assembly of a regenerable maize inbred line A188

Genome Biology ◽

10.1186/s13059-021-02396-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guifang Lin ◽

Cheng He ◽

Jun Zheng ◽

Dal-Hoe Koo ◽

Ha Le ◽

...

Keyword(s):

Inbred Line ◽

Genome Assembly ◽

Gene Function ◽

Maize Inbred Line ◽

Carotenoid Cleavage Dioxygenase ◽

Structural Variations ◽

Embryonic Callus ◽

Network Analyses ◽

A Genome ◽

Chromosome Level

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

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Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)

Agronomy ◽

10.3390/agronomy9100653 ◽

2019 ◽

Vol 9 (10) ◽

pp. 653 ◽

Cited By ~ 1

Author(s):

Bartosz Kozak ◽

Renata Galek ◽

Dariusz Zalewski ◽

Ewa Sawicka-Sienkiewicz

Keyword(s):

Genetic Map ◽

Genome Wide Association Study ◽

Reference Genome ◽

High Density ◽

Genetic Maps ◽

New Variety ◽

Model Legume ◽

Speed Up ◽

Trait Locus ◽

Next Generation Sequencing Ngs

Genetic maps are an essential tool for investigating molecular markers’ linkage with traits of agronomic importance. Breeders put a lot of emphasis on this type of markers, which are used in breeding programs implementation and speed up the process of a new variety development. In this paper, we construct a new, high-density linkage genetic map for Polish material on narrow-leafed lupin. The mapping population originated from crossing the Polish variety ‘Emir’ and the Belarusian breeding line ‘LAE-1’. A new map was constructed based on DArTseq markers—a new type of marker generated with the next-generation sequencing (NGS) technique. The map was built with 4602 markers, which are divided into 20 linkage groups, corresponding with the number of gametic chromosomes in narrow-leafed lupin. On the new map there are 1174 unique loci. The total length of all linkage group is 3042 cM. This map was compared to the reference genome of narrow-leafed lupin and the CDS sequence for model legume species: emphMedicago truncatula, emphLotus japonicus and Glycine max. Analysis revealed the presence of the DArTseq marker common for all investigated species. We were able to map 38 new, unplaced scaffolds on the new genetic map of narrow-leafed lupin. The high-density genetic map we received can be used for quantitative trait locus (QTL) mapping, genome-wide association study analysis and assembly of the reference genome for the whole genome sequencing (WGS) method

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Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

PeerJ ◽

10.7717/peerj.12390 ◽

2021 ◽

Vol 9 ◽

pp. e12390

Author(s):

Yaqun Zhang ◽

Chuantao Zhang ◽

Na Yao ◽

Jingxian Huang ◽

Xiangshan Sun ◽

...

Keyword(s):

Sex Determination ◽

Linkage Map ◽

Genetic Linkage ◽

Molecular Mechanisms ◽

Genetic Linkage Map ◽

Genotyping By Sequencing ◽

High Density ◽

Nucleotide Polymorphisms ◽

Penaeus Japonicus ◽

Genetic Mechanisms

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

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Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis )

Royal Society Open Science ◽

10.1098/rsos.172054 ◽

2018 ◽

Vol 5 (5) ◽

pp. 172054 ◽

Cited By ~ 5

Author(s):

Mimi Xie ◽

Yao Ming ◽

Feng Shao ◽

Jianbo Jian ◽

Yaoguang Zhang ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Restriction Site ◽

Genome Structure ◽

High Density ◽

Genetic Maps ◽

High Quality ◽

Silurus Meridionalis ◽

Map Construction ◽

High Density Linkage Map

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish ( Silurus meridionalis ). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.

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A SNP-Based Linkage Map and QTL Identification for Resistance to Yam Anthracnose Disease (YAD) in Water Yam (Dioscorea alata)

10.21203/rs.3.rs-26806/v1 ◽

2020 ◽

Author(s):

Kwabena Darkwa ◽

Paterne AGRE ◽

Bunmi Olasanmi ◽

Olufisayo Kolade ◽

Pierre Mournet ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

High Density ◽

Genetic Maps ◽

Dioscorea Alata ◽

Valuable Insight ◽

Phenotypic Variance ◽

Anthracnose Resistance ◽

Anthracnose Disease ◽

Water Yam

Abstract Background: Yam anthracnose disease (YAD) caused by Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Development of resistant cultivars have been a prime target for sustainable management of anthracnose in water yam. Molecular breeding tools are required to expedite the development of improved yam varieties. QTL analysis using high density genetic maps serve as a powerful tool to discover key locations of quantitave traits. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata.Results: In this study, two contrasting parents for yam anthracnose disease reaction and their 204 full- sib offspring were used to develop a high-density genetic linkage map with 3,257 SNP markers by the GBS technique. The total length of the consensus map was 1460.94 cM with an average of 163 markers per chromosome. Four QTLs were detected for anthracnose disease resistance in 4 locations on 3 chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 10 to 13%. Plant defense response genes including GDSL-like Lipase/Acylhydrolase, Protein kinase domain and F-box protein were also detected within the QTL regions. Conclusion: The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers and putative genes identified herewith form a relevant resource to apply marker-assisted selection as alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

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Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

PeerJ ◽

10.7717/peerj.12504 ◽

2021 ◽

Vol 9 ◽

pp. e12504

Author(s):

Guan Li ◽

Yichen Cheng ◽

Man Yin ◽

Jinyu Yang ◽

Jiezheng Ying ◽

...

Keyword(s):

Grain Yield ◽

Linkage Map ◽

Genetic Map ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Recombinant Inbred Line Population ◽

Recombinant Inbred ◽

High Density ◽

Rice Grain ◽

High Density Linkage Map

Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006–JD1007 and RM1148–RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.

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Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽

10.3390/horticulturae7120534 ◽

2021 ◽

Vol 7 (12) ◽

pp. 534

Author(s):

Zhijiang Wu ◽

Haiyan Deng ◽

Guidong Liang ◽

Xiaoying Ye ◽

Yonghua Qin ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Snp Markers ◽

High Density ◽

Genetic Maps ◽

Fleshy Fruit ◽

Whole Genome ◽

Genome Resequencing ◽

Hylocereus Undatus ◽

Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

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Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab142 ◽

2021 ◽

Author(s):

Elizabeth Popowski ◽

Susan J Thomson ◽

Mareika Knäbel ◽

Jibran Tahir ◽

Ross N Crowhurst ◽

...

Keyword(s):

Linkage Map ◽

Complex Traits ◽

Genotyping By Sequencing ◽

High Density ◽

Dry Matter Accumulation ◽

Production Traits ◽

Trait Locus ◽

And Storage ◽

High Density Linkage Map ◽

Green Kiwifruit

Abstract Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed A. chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa ‘Hayward’, is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. Limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3,686 and 3,940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis ‘Red5’ reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.

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Chromosome-level assembly of the mustache toad genome using third-generation DNA sequencing and Hi-C analysis

GigaScience ◽

10.1093/gigascience/giz114 ◽

2019 ◽

Vol 8 (9) ◽

Cited By ~ 7

Author(s):

Yongxin Li ◽

Yandong Ren ◽

Dongru Zhang ◽

Hui Jiang ◽

Zhongkai Wang ◽

...

Keyword(s):

Breeding Season ◽

Reference Genome ◽

Gene Families ◽

Sequencing Data ◽

High Quality ◽

Chromosome Conformation ◽

Functional Studies ◽

Sequencing Technologies ◽

A Genome ◽

Chromosome Level

Abstract Background The mustache toad, Vibrissaphora ailaonica, is endemic to China and belongs to the Megophryidae family. Like other mustache toad species, V. ailaonica males temporarily develop keratinized nuptial spines on their upper jaw during each breeding season, which fall off at the end of the breeding season. This feature is likely result of the reversal of sexual dimorphism in body size, with males being larger than females. A high-quality reference genome for the mustache toad would be invaluable to investigate the genetic mechanism underlying these repeatedly developing keratinized spines. Findings To construct the mustache toad genome, we generated 225 Gb of short reads and 277 Gb of long reads using Illumina and Pacific Biosciences (PacBio) sequencing technologies, respectively. Sequencing data were assembled into a 3.53-Gb genome assembly, with a contig N50 length of 821 kb. We also used high-throughput chromosome conformation capture (Hi-C) technology to identify contacts between contigs, then assembled contigs into scaffolds and assembled a genome with 13 chromosomes and a scaffold N50 length of 412.42 Mb. Based on the 26,227 protein-coding genes annotated in the genome, we analyzed phylogenetic relationships between the mustache toad and other chordate species. The mustache toad has a relatively higher evolutionary rate and separated from a common ancestor of the marine toad, bullfrog, and Tibetan frog 206.1 million years ago. Furthermore, we identified 201 expanded gene families in the mustache toad, which were mainly enriched in immune pathway, keratin filament, and metabolic processes. Conclusions Using Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level mustache toad genome. This work not only offers a valuable reference genome for functional studies of mustache toad traits but also provides important chromosomal information for wider genome comparisons.

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