Studying the Genetic Diversity of Yam Bean Using a New Draft Genome Assembly

Yam bean (Pachyrhizus erosus Rich. Ex DC.) is an underutilized leguminous crop which has been used as a food source across central America and Asia. It is adapted to a range of environments and is closely related to major leguminous food crops, offering the potential to understand the genetic basis of environmental adaptation, and it may be used as a source of novel genes and alleles for the improvement of other legumes. Here, we assembled a draft genome of P. erosus of 460 Mbp in size containing 37,886 gene models. We used this assembly to compare three cultivars each of P. erosus and the closely related P. tuberosus and identified 10,187,899 candidate single nucleotide polymorphisms (SNPs). The SNP distribution reflects the geographic origin and morphology of the individuals.

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The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

10.7287/peerj.preprints.1707v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jian-Zhi Huang ◽

Chih-Peng Lin ◽

Ting-Chi Cheng ◽

Ya-Wen Huang ◽

Yi-Jung Tsai ◽

...

Keyword(s):

Economic Value ◽

Draft Genome ◽

Floral Organ ◽

Cool Temperature ◽

Organ Development ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Draft Genome Assembly ◽

Genome Data ◽

Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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Genetic Differentiation of Verticillium dahliae Populations Recovered from Symptomatic and Asymptomatic Hosts

Phytopathology ◽

10.1094/phyto-06-20-0230-fi ◽

2020 ◽

pp. PHYTO-06-20-023

Author(s):

Laura S. Bautista-Jalón ◽

Omer Frenkel ◽

Leah Tsror (Lahkim) ◽

Glenna M. Malcolm ◽

Beth K. Gugino ◽

...

Keyword(s):

Genetic Differentiation ◽

Verticillium Dahliae ◽

Geographic Origin ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Weed Species ◽

Single Nucleotide ◽

Vegetative Compatibility Groups ◽

Main Research ◽

Research Goal

Verticillium dahliae is a soilborne fungal pathogen affecting many economically important crops that can also infect weeds and rotational crops with no apparent disease symptoms. The main research goal was to test the hypothesis that V. dahliae populations recovered from asymptomatic rotational crops and weed species are evolutionarily and genetically distinct from symptomatic hosts. We collected V. dahliae isolates from symptomatic and asymptomatic hosts growing in fields with histories of Verticillium wilt of potato in Israel and Pennsylvania (United States), and used genotyping-by-sequencing to analyze the evolutionary history and genetic differentiation between populations of different hosts. A phylogeny inferred from 26,934 single-nucleotide polymorphisms (SNPs) in 126 V. dahliae isolates displayed a highly clonal structure correlated with vegetative compatibility groups, and isolates grouped in lineages 2A, 2B824, 4A, and 4B, with 77% of the isolates in lineage 4B. The lineages identified in this study were differentiated by host of origin; we found 2A, 2B824, and 4A only in symptomatic hosts but isolates from asymptomatic hosts (weeds, oat, and sorghum) grouped exclusively within lineage 4B, and were genetically indistinguishable from 4B isolates sampled from symptomatic hosts (potato, eggplant, and avocado). Using coalescent analysis of 158 SNPs of lineage 4B, we inferred a genealogy with clades that correlated with geographic origin. In contrast, isolates from asymptomatic and symptomatic hosts shared some of the same haplotypes and were not differentiated. We conclude that asymptomatic weeds and rotational hosts may be potential reservoirs for V. dahliae populations of lineage 4B, which are pathogenic to many cultivated hosts.

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Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

Nutrients ◽

10.3390/nu12092689 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2689

Author(s):

Augusto Anguita-Ruiz ◽

Concepción M. Aguilera ◽

Ángel Gil

Keyword(s):

Genetic Basis ◽

Human Populations ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genotype Frequencies ◽

Genetic Mechanisms ◽

Visualization Tools ◽

Available Information ◽

Static World ◽

Interactive Resources

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

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Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

GigaScience ◽

10.1093/gigascience/giz115 ◽

2019 ◽

Vol 8 (10) ◽

Cited By ~ 3

Author(s):

Bo Song ◽

Yue Song ◽

Yuan Fu ◽

Elizabeth Balyejusa Kizito ◽

Sandra Ndagire Kamenya ◽

...

Keyword(s):

Disease Resistance ◽

Single Nucleotide Polymorphisms ◽

Drought Tolerance ◽

Resistance Genes ◽

Draft Genome ◽

Disease Resistance Genes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Protein Coding Genes

Abstract Background The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

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Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

Current Zoology ◽

10.1093/czoolo/61.1.146 ◽

2015 ◽

Vol 61 (1) ◽

pp. 146-154 ◽

Cited By ~ 26

Author(s):

Brian K. Hand ◽

Tyler D. Hether ◽

Ryan P. Kovach ◽

Clint C. Muhlfeld ◽

Stephen J. Amish ◽

...

Keyword(s):

Genome Assembly ◽

Native Species ◽

Draft Genome ◽

Cutthroat Trout ◽

Rad Sequencing ◽

Nucleotide Polymorphisms ◽

Introduced Fish ◽

Draft Genome Assembly ◽

Native Populations ◽

Diagnostic Snps

Abstract Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understanding the effects of hybridization on native populations (e.g., fitness consequences) requires numerous species-diagnostic loci distributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphisms (SNPs) that are diagnostic between rainbow trout (RBT, Oncorhynchus mykiss), the world’s most widely introduced fish, and native westslope cutthroat trout (WCT, O. clarkii lewisi) in the northern Rocky Mountains, USA. We advanced previous work that identified 4,914 species-diagnostic loci by using longer sequence reads (100 bp vs. 60 bp) and a larger set of individuals (n = 84). We sequenced RAD libraries for individuals from diverse sampling sources, including native populations of WCT and hatchery broodstocks of WCT and RBT. We also took advantage of a newly released reference genome assembly for RBT to align our RAD loci. In total, we discovered 16,788 putatively diagnostic SNPs, 10,267 of which we mapped to anchored chromosome locations on the RBT genome. A small portion of previously discovered putative diagnostic loci (325 of 4,914) were no longer diagnostic (i.e., fixed between species) based on our wider survey of non-hybridized RBT and WCT individuals. Our study suggests that RAD loci mapped to a draft genome assembly could provide the marker density required to identify genes and chromosomal regions influencing selection in admixed populations of conservation concern and evolutionary interest.

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Draft Genome Sequences of Two Extensively Drug-Resistant Strains ofMycobacterium tuberculosisBelonging to the Euro-American S Lineage

Genome Announcements ◽

10.1128/genomea.01771-15 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 2

Author(s):

Lesibana A. Malinga ◽

Thomas Abeel ◽

Christopher A. Desjardins ◽

Talent C. Dlamini ◽

Gail Cassell ◽

...

Keyword(s):

Draft Genome ◽

Drug Efflux ◽

Drug Resistant ◽

Nucleotide Polymorphisms ◽

Genome Sequences ◽

Single Nucleotide ◽

Resistant Tuberculosis ◽

Extensively Drug Resistant ◽

Resistant Strains ◽

Drug Resistant Strains

We report the whole-genome sequencing of two extensively drug-resistant tuberculosis strains belonging to the Euro-American S lineage. The RSA 114 strain showed single-nucleotide polymorphisms predicted to have drug efflux activity.

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Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes

10.1101/2020.11.13.382077 ◽

2020 ◽

Author(s):

Bruce A. Williamson-Benavides ◽

Richard Sharpe ◽

Grant Nelson ◽

Eliane T. Bodah ◽

Lyndon D. Porter ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Fusarium Solani ◽

Root Rot ◽

Genetic Basis ◽

Gene Pyramiding ◽

Interval Mapping ◽

Differentially Expressed ◽

Nucleotide Polymorphisms ◽

Resistance Qtls ◽

Single Nucleotide

AbstractPisum sativum (pea) yields have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome V explained 14.76 % of the variance with a confidence interval of 10.36 cM. The other four QTLs located on chromosomes II, III, and V, explained 5.26–8.05 % of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

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Genomic Determinants of Hypertension With a Focus on Metabolomics and the Gut Microbiome

American Journal of Hypertension ◽

10.1093/ajh/hpaa022 ◽

2020 ◽

Vol 33 (6) ◽

pp. 473-481

Author(s):

Panayiotis Louca ◽

Cristina Menni ◽

Sandosh Padmanabhan

Keyword(s):

Blood Pressure ◽

Genetic Basis ◽

Salt Water ◽

Nucleotide Polymorphisms ◽

Pressure Regulation ◽

Single Nucleotide ◽

Multiple Factors ◽

Single Marker ◽

Genomic Studies ◽

Diet And Lifestyle

Abstract Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of Mendelian forms of syndromic hypotension and hypertension (HTN) have all been linked to mutations in genes whose encoded proteins regulate salt–water balance in the kidney, supporting the primacy of the kidneys in blood pressure regulation. There are more than 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome, and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet, and microbial ecology in humans in the causation of essential hypertension.

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A systematic study of single-nucleotide polymorphisms in theA4GALTgene suggests a molecular genetic basis for the P1/P2blood groups

Transfusion ◽

10.1111/trf.12771 ◽

2014 ◽

Vol 54 (12) ◽

pp. 3222-3231 ◽

Cited By ~ 14

Author(s):

Yin-Ju Lai ◽

Wan-Yi Wu ◽

Chen-Ming Yang ◽

Li-Rong Yang ◽

Chen-Chung Chu ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Systematic Study ◽

Genetic Basis ◽

Molecular Genetic ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Molecular Genetic Basis

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Computational analysis of SNPs and INDELs in cluster bean cultivars involved in multiple trait expression

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.80.2.8 ◽

2020 ◽

Vol 80 (02) ◽

Author(s):

Sarika Sahu ◽

Tanmaya Kumar Sahu ◽

Sabri Ghosal ◽

Kishor Gaikwad ◽

A. R. Rao

Keyword(s):

Draft Genome ◽

Plant Biotechnology ◽

New Delhi ◽

Cyamopsis Tetragonoloba ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Multiple Trait ◽

Single Nucleotide ◽

Breeding Programs ◽

Cluster Bean

SNPs (Single Nucleotide Polymorphisms) are extensively used in plant breeding programs because of their automation and high precision in allele calling. In the present study, transcriptomes of three cultivars of Cyamopsis tetragonoloba, namely, RGC-936, RGC-1066 and M-18 were analysed for the identification of SNPs and Indels using the recently assembled draft genome made available by National Institute of Plant Biotechnology, New Delhi. Besides, a comparison among the identified SNPs and indels of three cultivars was made to mine out the cultivar specific SNPs and indels as well as common markers among the cultivars. In addition, an online database, cbSIR, was developed based on the markers populated from the said cultivars of cluster bean (http://webapp.cabgrid.res.in/clb_ce/index.php). The results reveal that highest number of SNPs (10279) were present in cultivar RGC-1066 followed by RGC-1066 (9714) and M-18 (7933). The detected SNPs were subjected to functional annotation. In a similar way, Indels were also identified and functionally annotated. Predictions were made based on the involvement of SNP/Indel possessing genes in the expression of multiple traits such as gum production, auxin transport, disease resistance in the three cultivars of cluster bean.

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