scholarly journals Nucleotide Diversity of the Maize ZmCNR13 Gene and Association With Ear Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhihao Zuo ◽  
Yue Lu ◽  
Minyan Zhu ◽  
Rujia Chen ◽  
Enying Zhang ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Inbred Lines ◽  
Gene Encoding ◽  
Selection Signature ◽  
Exon 2 ◽  
Coding Regions ◽  
Natural Variations ◽  
Phenotypic Variations ◽  
Maize Domestication ◽  
Maize Ear

The maize (Zea mays L.) ZmCNR13 gene, encoding a protein of fw2.2-like (FWL) family, has been demonstrated to be involved in cell division, expansion, and differentiation. In the present study, the genomic sequences of the ZmCNR13 locus were re-sequenced in 224 inbred lines, 56 landraces and 30 teosintes, and the nucleotide polymorphism and selection signature were estimated. A total of 501 variants, including 415 SNPs and 86 Indels, were detected. Among them, 51 SNPs and 4 Indels were located in the coding regions. Although neutrality tests revealed that this locus had escaped from artificial selection during the process of maize domestication, the population of inbred lines possesses lower nucleotide diversity and decay of linkage disequilibrium. To estimate the association between sequence variants of ZmCNR13 and maize ear characteristics, a total of ten ear-related traits were obtained from the selected inbred lines. Four variants were found to be significantly associated with six ear-related traits. Among them, SNP2305, a non-synonymous mutation in exon 2, was found to be associated with ear weight, ear grain weight, ear diameter and ear row number, and explained 4.59, 4.61, 4.31, and 8.42% of the phenotypic variations, respectively. These results revealed that natural variations of ZmCNR13 might be involved in ear development and can be used in genetic improvement of maize ear-related traits.

scholarly journals Nucleotide Diversity and Association Analysis of ZmMADS60 with Root Length in the Maize Seedling Stage

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 342
Author(s):  
Pengcheng Li ◽  
Zhenzhen Ge ◽  
Houmiao Wang ◽  
Jie Wei ◽  
Yunyun Wang ◽  
...  
Keyword(s):  
Association Analysis ◽  
Root Length ◽  
Nucleotide Diversity ◽  
Lateral Roots ◽  
Primary Root ◽  
Root System Architecture ◽  
Inbred Lines ◽  
Seedling Stage ◽  
Functional Markers ◽  
Maize Domestication

Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity and natural variations associated with root length. Nucleotide diversity and neutral tests revealed that ZmMADS60 might be selected in domestication and improvement processes. ZmMADS60 in maize retained only 40.1% and 66.9% of the nucleotide diversity found in teosinte and landrace, respectively. Gene-based association analysis of inbred lines identified nine variants that were significantly associated with primary root length (PRL), lateral root length (LRL), root length between 0 mm and 0.5 mm in diameter (RL005) and total root length (TRL). One single-nucleotide polymorphism SNP1357 with pleiotropic effects was significantly associated with LRL, RL005 and TRL. The frequency of the increased allele T decreased from 68.8% in teosintes to 52.9% and 38.9% in the landrace and inbred lines, respectively. The frequency of the increased allele of another significant SNP723 associated with PRL also decreased during the maize domestication and improvement processes. The results of this study reveal that ZmMADS60 may be involved in the elongation of primary and lateral roots in the seedling stage and that significant variants can be used to develop functional markers to improve root length in maize.

Development and validation of breeder-friendly functional markers of sugary1 gene encoding starch-debranching enzyme affecting kernel sweetness in maize (Zea mays)

2019 ◽  
Vol 70 (10) ◽  
pp. 868 ◽  
Author(s):  
Rashmi Chhabra ◽  
Firoz Hossain ◽  
Vignesh Muthusamy ◽  
Aanchal Baveja ◽  
Brijesh K. Mehta ◽  
...  
Keyword(s):  
Zea Mays ◽  
Sweet Corn ◽  
Inbred Lines ◽  
Recessive Allele ◽  
Functional Markers ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Gene Encoding ◽  
Exon 2 ◽  
Development And Validation

The sweet corn variety of maize (Zea mays L.) has become popular worldwide. The recessive allele of sugary1 (su1) encoding starch de-branching enzyme has been much used for sweet corn cultivar development. Here, we aimed to develop su1-based functional marker(s) by using six diverse inbred lines of sugary type and five inbred lines of wild type, and using 27 overlapping primers. In total, 12 indels (insertion and deletion) and 96 SNPs (single nucleotide polymorphisms) were identified that clearly differentiated the dominant and recessive allele of su1. Among these, a 36-bp indel (at position 1247) in the promoter region included a TATA-box, and a 6-bp indel (at position 6456) in intron-10 was predicted to have SRp40 exon-splicing enhancer. Nucleotide substitution in exon-2 at position 2703 (SNP-2703) was involved in C to G mutation leading to conversion of phenylalanine to leucine. The 6-bp and 36-bp indels and SNP-2703 were used to develop breeder-friendly codominant markers: SuDel6-FR, SuDel36-FR and SNP2703-CG-85/89. All three markers were validated in five F2 populations, and SuDel36-FR and SNP2703-CG-85/89 were validated in a set of 230 diverse inbreds having both mutant and wild-type alleles of Su1. This is the first report of development and validation of universal functional markers for su1. These markers (SuDel36-FR and SNP2703-CG-85/89) assume great significance in marker-assisted breeding program.

scholarly journals Defining the Role of the MADS-Box Gene, Zea Agamous-like1, a Target of Selection During Maize Domestication

2017 ◽  
Vol 109 (3) ◽  
pp. 333-338 ◽  
Author(s):  
David M Wills ◽  
Zhou Fang ◽  
Alessandra M York ◽  
James B Holland ◽  
John F Doebley
Keyword(s):  
Flowering Time ◽  
Nucleotide Diversity ◽  
Selection Candidate ◽  
Mads Box ◽  
Multiple Traits ◽  
Recombinant Chromosome ◽  
Mads Box Gene ◽  
Maize Domestication ◽  
Maize Ear

Abstract Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.

scholarly journals Natural Variation and Domestication Selection of ZmPGP1 Affects Plant Architecture and Yield-Related Traits in Maize

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 664
Author(s):  
Pengcheng Li ◽  
Jie Wei ◽  
Houmiao Wang ◽  
Yuan Fang ◽  
Shuangyi Yin ◽  
...  
Keyword(s):  
Natural Variation ◽  
Plant Architecture ◽  
Nucleotide Diversity ◽  
Inbred Lines ◽  
Leaf Angle ◽  
Functional Markers ◽  
Kernel Length ◽  
Domestication Selection ◽  
Maize Domestication ◽  
Selection Of

ZmPGP1, involved in the polar auxin transport, has been shown to be associated with plant height, leaf angle, yield traits, and root development in maize. To explore natural variation and domestication selection of ZmPGP1, we re-sequenced the ZmPGP1 gene in 349 inbred lines, 68 landraces, and 32 teosintes. Sequence polymorphisms, nucleotide diversity, and neutral tests revealed that ZmPGP1 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 11 variants significantly associated with 4 plant architecture and 5 ear traits. SNP1473 was the most significant variant for kernel length and ear grain weight. The frequency of an increased allele T was 40.6% in teosintes, and it was enriched to 60.3% and 89.1% during maize domestication and improvement. This result revealed that ZmPGP1 may be selected in the domestication and improvement process, and significant variants could be used to develop functional markers to improve plant architecture and ear traits in maize.

scholarly journals Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 29
Author(s):  
Lilia González-Cerón ◽  
José Cebrián-Carmona ◽  
Concepción M. Mesa-Valle ◽  
Federico García-Maroto ◽  
Frida Santillán-Valenzuela ◽  
...  
Keyword(s):  
Amino Acid ◽  
B Cell ◽  
Plasmodium Vivax ◽  
Nucleotide Diversity ◽  
Protective Antigen ◽  
Balancing Selection ◽  
Southern Mexico ◽  
Exon 2 ◽  
Exon 1 ◽  
Tajima’S D

Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima’s D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima’s D, β-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.

scholarly journals Natural variations in the P-type ATPase heavy metal transporter ZmCd1 controlling cadmium accumulation in maize grains

2021 ◽  
Author(s):  
Bin Tang ◽  
Meijie Luo ◽  
Yunxia Zhang ◽  
Huanle Guo ◽  
Jingna Li ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Molecular Markers ◽  
Genome Wide Association Study ◽  
Inbred Lines ◽  
Cd Accumulation ◽  
A Genome ◽  
Maize Varieties ◽  
Natural Variations ◽  
Maize Grain ◽  
P Type

SummaryCadmium (Cd) accumulation in maize grains is detrimental to human health. Developing maize varieties with low-Cd contents via marker-assisted selection is important for ensuring the production of maize grains safe for consumption. However, the key gene controlling maize grain Cd accumulation has not been cloned. In this study, we identified two major loci for maize grain Cd accumulation (qCd1 and qCd2) on chromosome 2 during a genome-wide association study (GWAS). The qCd1 locus was analyzed by bulked segregant RNA-seq and fine mapping with a biparental segregating population of Jing724 (low-Cd line) and Mo17 (high-Cd line). The ZmCd1 candidate gene in the qCd1 locus encodes a vacuolar membrane-localized heavy metal P-type ATPase transporter, ZmHMA3, which is orthologous to the tonoplast Cd transporter OsHMA3. Genomic DNA sequence and transcript analyses suggested that a transposon in intron 1 of ZmCd1 is responsible for the abnormal amino acid sequence in Mo17. An EMS mutant analysis and an allelism test confirmed ZmCd1 influences maize grain Cd accumulation. The natural variations in ZmCd1 were used to develop four PCR-based molecular markers, which revealed five ZmCd1 haplotypes in the GWAS population. The molecular markers were also used to predict the grain Cd contents in commonly cultivated maize germplasms in China. The predicted Cd contents for 36 inbred lines and 13 hybrids were consistent with the measured Cd contents. Furthermore, several low-Cd elite inbred lines and hybrids were identified, including Jing2416, MC01, Jingnonke728, and Jingke968. Therefore, the molecular markers developed in this study are applicable for molecular breeding and developing maize varieties with low grain Cd contents.

A new polymorphism (N21D) in the exon 2 of the human MDR1 gene encoding the P-glycoprotein

2000 ◽  
Vol 15 (5) ◽  
pp. 486-486 ◽  
Author(s):  
Xavier Decl�ves ◽  
Sylvie Chevillard ◽  
Charlotte Charpentier ◽  
Philippe Vielh ◽  
Jean-Louis Laplanche
Keyword(s):  
Mdr1 Gene ◽  
Gene Encoding ◽  
Exon 2 ◽  
P Glycoprotein ◽  
Human Mdr1

scholarly journals Epidemiological aspects of group B streptococci of bovine and human origin

1996 ◽  
Vol 117 (3) ◽  
pp. 417-422 ◽  
Author(s):  
N. E. Jensen ◽  
F. M. Aarestrup
Keyword(s):  
Streptococcus Agalactiae ◽  
Double Diffusion ◽  
Restriction Enzymes ◽  
Group B Streptococci ◽  
Gene Encoding ◽  
Genetic Changes ◽  
Lactose Fermentation ◽  
Phenotypic Variations ◽  
Group B ◽  
Reference Strains

SummaryRestriction fragment length polymorphism of the gene encoding rRNA (ribotyping) was used in combination with conventional epidemiological markers to study phenotypic variations amongStreptococcus agalactiaeof bovine origin and the possible epidemiological interrelationship between the bovine and human reservoirs ofStreptococcus agalactiae.The bovine material constituted 53 strains (9 antigen combinations) isolated from 11 herds. Herds with a uniform as well as heterogenic antigenic pattern were included. Furthermore, strains isolated in the course of time from the same persistently infected quarters were examined. The human material constituted 16 strains, 4 each of 4 serotypes, isolated from healthy carriers. Finally, nine serotype- and the group reference strains were examined. All strains were serotyped by double diffusion in agarose gel, biotyped (lactose ±), and ribotyped using two restriction enzymes,HindIII andHhaI.All isolates could be typed by ribotyping and seven ribotypes were identified among the reference strains. The restriction enzymes used alone or in combination gave typing results that allowed discrimination between and within serotype. Combined use of serotype,HindIII andHhaI ribotypes produced 11 types among the 16 human strains. Ribotype analysis discriminated between herds infected with the same serotype. Strains of varying antigenic patterns from the same herd had the same ribotype. Phenotypic variations in serotype observed in persistent intramammary infection were not related to genetic changes as monitored by ribotype. Two ribotypes were represented among both bovine and human strains. The discriminating capability of lactose fermentation was of limited value.

scholarly journals Characterization of the gene for mp20: a Drosophila muscle protein that is not found in asynchronous oscillatory flight muscle.

1989 ◽  
Vol 108 (2) ◽  
pp. 521-531 ◽  
Author(s):  
A Ayme-Southgate ◽  
P Lasko ◽  
C French ◽  
M L Pardue
Keyword(s):  
Calcium Binding ◽  
Muscle Protein ◽  
Primary Cultures ◽  
Specific Protein ◽  
Gene Encoding ◽  
Significant Similarity ◽  
Coding Regions ◽  
Flight Muscles ◽  
Calcium Binding Sites

A Drosophila melanogaster gene encoding a muscle specific protein was isolated by differential screening with RNA from primary cultures of myotubes. The gene encodes a 20-kD protein, muscle protein 20 (mp20), that is not detected in the asynchronous oscillatory flight muscles, but is found in most, if not all, other muscles (the synchronous muscles). The sequence of the protein, deduced from the DNA, contains two regions of 12 amino acids with significant similarity to high-affinity calcium-binding sites of other proteins. This protein is easily extracted from the contractile apparatus and thus does not seem to be a tightly bound structural component. The gene (located in polytene region 49F 9-13) is unique in the D. melanogaster genome and yields two transcripts, 1.0 and 0.9 kb long. The levels of the two transcripts are regulated differently during development, yet the coding regions of the two transcripts are identical.

scholarly journals Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions

2021 ◽  
Author(s):  
Magnus Alm Rosenblad ◽  
Anna Abramova ◽  
Ulrika Lind ◽  
Páll Ólason ◽  
Stefania Giacomello ◽  
...  
Keyword(s):  
Genome Size ◽  
Nucleotide Diversity ◽  
Reference Genome ◽  
Size Estimation ◽  
Marine Biotechnology ◽  
Coding Regions ◽  
Repeat Content ◽  
Genomic Knowledge ◽  
Octopamine Receptor ◽  
Balanus Improvisus

AbstractBarnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.

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