Identification of Markers Associated with Yield Traits and Morphological Features in Maize (Zea mays L.)

Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium in molecular plant breeding. The aim of this study was the identification of single nucleotide polymorphisms (SNPs) and SilicoDArT markers associated with yield traits and morphological features in maize. Plant material constituted inbred lines. The field experiment with inbred lines was established on 10 m2 plots in a set of complete random blocks in three replicates. We observed 22 quantitative traits. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis applied to all markers) and modeled by random effects. As a result of mapping, 969 markers (346 SNPs and 623 SilocoDArT) were selected from 49,911 identified polymorphic molecular markers, which were significantly associated with the analyzed morphological features and yield structure traits. Markers associated with five or six traits were selected during further analyses, including SilicoDArT 4591115 (anthocyanin coloration of anthers, length of main axis above the highest lateral branch, cob length, number of grains per cob, weight of fresh grains per cob and weight of fresh grains per cob at 15% moisture), SilicoDArT 7059939 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, time of silk emergence—50% of flowering plants, anthocyanin coloration of anthers and cob diameter), SilicoDArT 5587991 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, anthocyanin coloration of anthers, curvature of lateral branches and number of rows of grain). The two genetic similarity dendrograms between the inbred lines were constructed based on all significant SNPs and SilicoDArT markers. On both dendrograms lines clustered according to the kernel structure (flint, dent) and origin. The selected markers may be useful in predicting hybrid formulas in a heterosis culture. The present study demonstrated that molecular SNP and Silico DArT markers could be used in this species to group lines in terms of origin and lines with incomplete origin data. They can also be useful in maize in predicting the hybrid formula and can find applications in the selection of parental components for heterosis crossings.

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Identification and Confirmation of Loci Associated With Canopy Wilting in Soybean Using Genome-Wide Association Mapping

Frontiers in Plant Science ◽

10.3389/fpls.2021.698116 ◽

2021 ◽

Vol 12 ◽

Author(s):

Siva K. Chamarthi ◽

Avjinder S. Kaler ◽

Hussein Abdel-Haleem ◽

Felix B. Fritschi ◽

Jason D. Gillman ◽

...

Keyword(s):

Drought Tolerance ◽

Association Mapping ◽

Candidate Genes ◽

Stress Responses ◽

Water Conservation ◽

Production Systems ◽

Block Design ◽

Plant Stress ◽

Significant Snps ◽

Nucleotide Polymorphisms

Drought causes significant soybean [Glycine max (L.) Merr.] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of this study were to confirm previously reported soybean loci and to identify novel loci associated with canopy wilting (CW) using a panel of 200 diverse maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site-years using an augmented incomplete block design with three replications under irrigated and rain-fed treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with CW that likely tagged 152 loci. This includes 87 SNPs coincident with previous studies that likely tagged 68 loci and 101 novel SNPs that likely tagged 84 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research studies to predict CW in different genotypes and environments. A positive relationship (P ≤ 0.05;0.37 ≤ r ≤ 0.5) was found between observed CW and GEBVs. In the vicinity of 188 significant SNPs, 183 candidate genes were identified for both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 SNPs were present within genes coding for proteins with biological functions involved in plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and, as candidates for genomic selection, enhancing soybean drought tolerance.

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NAM population – a novel genetic resource for soybean improvement: development and characterization for yield and attributing traits

Plant Genetic Resources ◽

10.1017/s1479262119000352 ◽

2019 ◽

Vol 17 (6) ◽

pp. 545-553 ◽

Cited By ~ 1

Author(s):

Shivakumar Maranna ◽

Giriraj Kumawat ◽

Vennampally Nataraj ◽

C. Gireesh ◽

Sanjay Gupta ◽

...

Keyword(s):

Genetic Diversity ◽

Grain Yield ◽

Association Mapping ◽

Genetic Resource ◽

Recombinant Inbred Lines ◽

Principal Component ◽

Central India ◽

Inbred Lines ◽

Yellow Mosaic Virus ◽

Yield Potential

AbstractNested association mapping (NAM) captures the best features of both linkage and association mapping and enables the high power and high resolution of quantitative trait locus mapping through joint linkage-association analysis. In the current study, NAM population was developed by hybridizing JS 335, a popular variety of central India with 20 diverse soybean genotypes. The parents used in the study have various traits of economic importance such as drought and water-logging tolerance, bacterial pustule and yellow mosaic virus resistance, wider adaptability, resistance to mechanical damage and higher yield potential. High variability in the F2 populations of 20 crosses for grain yield and days to maturity indicated scope for development of high-yielding varieties. Genetic variability studies, correlation, regression, principal component analysis (PCA) and genetic diversity analyses were carried out in 900 NAM-recombinant inbred lines (RILs) derived from 11 crosses. Correlation and regression analysis indicated a significant positive effect of biomass, pods/plant, harvest index, branches/plant, nodes/plant and plant height on grain yield. Genetic diversity analysis grouped 900 NAM-RILs into 10 clusters. PCA revealed first two principal components to explain 63.78% of total variation mostly contributed by grain yield, biomass and number of pods. The inbred lines developed in this study will serve as an elite soybean genetic resource in understanding the genetic architecture underlying different traits of economic significance.

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DArTseq-Based High-Throughput SilicoDArT and SNP Markers Applied for Association Mapping of Genes Related to Maize Morphology

International Journal of Molecular Sciences ◽

10.3390/ijms22115840 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5840

Author(s):

Agnieszka Tomkowiak ◽

Jan Bocianowski ◽

Julia Spychała ◽

Joanna Grynia ◽

Aleksandra Sobiech ◽

...

Keyword(s):

Next Generation Sequencing ◽

Plant Material ◽

Snp Markers ◽

Morphological Features ◽

Chromosome 7 ◽

Restriction Enzyme Digestion ◽

Nucleotide Polymorphisms ◽

Next Generation ◽

Lateral Branches ◽

Generation Sequencing

Today, agricultural productivity is essential to meet the needs of a growing population, and is also a key tool in coping with climate change. Innovative plant breeding technologies such as molecular markers, phenotyping, genotyping, the CRISPR/Cas method and next-generation sequencing can help agriculture meet the challenges of the 21st century more effectively. Therefore, the aim of the research was to identify single-nucleotide polymorphisms (SNPs) and SilicoDArT markers related to select morphological features determining the yield in maize. The plant material consisted of ninety-four inbred lines of maize of various origins. These lines were phenotyped under field conditions. A total of 14 morphological features was analyzed. The DArTseq method was chosen for genotyping because this technique reduces the complexity of the genome by restriction enzyme digestion. Subsequently, short fragment sequencing was used. The choice of a combination of restrictases allowed the isolation of highly informative low copy fragments of the genome. Thanks to this method, 90% of the obtained DArTseq markers are complementary to the unique sequences of the genome. All the observed features were normally distributed. Analysis of variance indicated that the main effect of lines was statistically significant (p < 0.001) for all 14 traits of study. Thanks to the DArTseq analysis with the use of next-generation sequencing (NGS) in the studied plant material, it was possible to identify 49,911 polymorphisms, of which 33,452 are SilicoDArT markers and the remaining 16,459 are SNP markers. Among those mentioned, two markers associated with four analyzed traits deserved special attention: SNP (4578734) and SilicoDArT (4778900). SNP marker 4578734 was associated with the following features: anthocyanin coloration of cob glumes, number of days from sowing to anthesis, number of days from sowing to silk emergence and anthocyanin coloration of internodes. SilicoDArT marker 4778900 was associated with the following features: number of days from sowing to anthesis, number of days from sowing to silk emergence, tassel: angle between the axis and lateral branches and plant height. Sequences with a length of 71 bp were used for physical mapping. The BLAST and EnsemblPlants databases were searched against the maize genome to identify the positions of both markers. Marker 4578734 was localized on chromosome 7, the closest gene was Zm00001d022467, approximately 55 Kb apart, encoding anthocyanidin 3-O-glucosyltransferase. Marker 4778900 was located on chromosome 7, at a distance of 45 Kb from the gene Zm00001d045261 encoding starch synthase I. The latter observation indicated that these flanking SilicoDArT and SNP markers were not in a state of linkage disequilibrium.

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Association Mapping for Drought Tolerance and Yield-Related Traits in Cowpea Accessions

10.20944/preprints202010.0001.v1 ◽

2020 ◽

Author(s):

Gabriel Vusanimuzi Nkomo ◽

Moosa Sedibe ◽

Maletsema Alina Mofokeng ◽

Rian Pierneef

Keyword(s):

Drought Tolerance ◽

Association Mapping ◽

Linear Model ◽

Genotyping By Sequencing ◽

Mixed Linear Model ◽

Snp Markers ◽

P Value ◽

Nucleotide Polymorphisms ◽

Single Marker ◽

Peak Of Delta

The objective of this study were to conduct association mapping for drought tolerance at the seedling stage and yield-related traits. 60 cowpea accessions were used in the study. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Association mapping was conducted using single-marker regression (SMR) in Q Gene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. The population of the cowpea accessions were analysed using STRUCTURE 2.3.4 and the peak of delta K in the greenhouse showed seven population types, whereas the peak of delta K in the glasshouse indicated the presence of six population types. One SNP marker, 14083649|F|0-9 was associated with NP with a p value <0.001. Fifty SNP markers were associated with PWT at p <0.001. Four SNP markers, 14074781|F|0-16, 100047392|F|0-36, 14083801|F|0-28 and 100051488|F|0-49 were associated with AVSPD at p <0.001. SNP markers, 14074781|F|0-16, 14083801|F|0-28 and 100051488|F|0-49 were associated with PL at P <0.001. Five SNP markers, 100047392|F|0-36, 14083801|F|0-28, 100072738|F|0-34, 14076881|F|0-49 and 14076881|F|0-49 were associated with PWDTH at p <0.001. The 65 SNP markers identified can be used in cowpea molecular breeding to select for AVSPD, NP, PL, PWDTH, PWT, and RR through marker assisted selection (MAS).

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Association between the Polymorphisms of fads2a and fads2b and Poly-Unsaturated Fatty Acids in Common Carp (Cyprinus carpio)

Animals ◽

10.3390/ani11061780 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1780

Author(s):

Yan Zhang ◽

Xiao-Qing Sun ◽

Yu-Qing Ye ◽

Qi Wang ◽

Qing-Song Li ◽

...

Keyword(s):

Common Carp ◽

Unsaturated Fatty Acids ◽

Major Gene ◽

Fatty Acid Desaturase ◽

Mixed Linear Model ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Food Fish ◽

Rate Limiting ◽

Fatty Acid Desaturase 2

Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one fads2, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (fads2a and fads2b). The associations between the contents of different PUFAs and the polymorphisms of fads2a and fads2b have not been studied. The contents of 12 PUFAs in common carp individuals were measured, and the polymorphisms in the coding sequences of fads2a and fads2b were screened. We identified five coding single nucleotide polymorphisms (cSNPs) in fads2a and eleven cSNPs in fads2b. Using the mixed linear model and analysis of variance, a synonymous fads2a cSNP was significantly associated with the content of C20:3n-6. One non-synonymous fads2b cSNP (fads2b.751) and one synonymous fads2b cSNP (fads2b.1197) were associated with the contents of seven PUFAs and the contents of six PUFAs, respectively. The heterozygous genotypes in both loci were associated with higher contents than the homozygous genotypes. The fads2b.751 genotype explained more phenotype variation than the fads2b.1197 genotype. These two SNPs were distributed in one haplotype block and associated with the contents of five common PUFAs. These results suggested that fads2b might be the major gene responding to common carp PUFA contents and that fads.751 might be the main effect SNP. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp.

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Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽

10.3390/genes12060832 ◽

2021 ◽

Vol 12 (6) ◽

pp. 832

Author(s):

Nina Moravčíková ◽

Radovan Kasarda ◽

Radoslav Židek ◽

Luboš Vostrý ◽

Hana Vostrá-Vydrová ◽

...

Keyword(s):

Demographic History ◽

Genome Structure ◽

Principal Component ◽

Genetic Distances ◽

Nucleotide Polymorphisms ◽

German Shepherd ◽

German Shepherd Dog ◽

Genome Wide ◽

Scale Population ◽

History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

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Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments

Plant Cell & Environment ◽

10.1111/pce.12096 ◽

2013 ◽

Vol 36 (10) ◽

pp. 1871-1887 ◽

Cited By ~ 40

Author(s):

ALEXANDER STRIGENS ◽

NICLAS M. FREITAG ◽

XAVIER GILBERT ◽

CHRISTOPH GRIEDER ◽

CHRISTIAN RIEDELSHEIMER ◽

...

Keyword(s):

Association Mapping ◽

Field Experiments ◽

Chilling Tolerance ◽

Inbred Lines ◽

Growth Chamber ◽

Maize Inbred Lines

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A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

Science & Technology Journal ◽

10.22232/stj.2021.09.01.09 ◽

2021 ◽

Vol 9 (1) ◽

pp. 49-55

Author(s):

Vanlal hruaia ◽

◽

Lal rinmuana ◽

J Lalbiaknunga ◽

Laldinfeli Ralte

Keyword(s):

Phylogenetic Tree ◽

Evolutionary Relationship ◽

Cladistic Analysis ◽

Morphological Characters ◽

Flowering Plants ◽

Morphological Features ◽

Total Evidence ◽

Pictorial Representation ◽

Phenetic Analysis ◽

Morphological Relationship

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

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Association Mapping for Improvement of Quantitative Traits in Plant Breeding Populations

Nepal Journal of Biotechnology ◽

10.3126/njb.v2i1.5686 ◽

1970 ◽

Vol 2 (1) ◽

pp. 72-89

Author(s):

Umesh R Rosyara ◽

Bal K Joshi

Keyword(s):

Association Mapping ◽

Plant Breeding ◽

Fine Mapping ◽

Quantitative Trait ◽

Human Genetics ◽

Crop Improvement ◽

Nucleotide Polymorphisms ◽

Breeding Populations ◽

Validation Of Results ◽

Mapping Populations

DNA-based molecular markers have been extensively utilized for mapping of genes and quantitative trait loci (QTL) of interest based on linkage analysis in mapping populations. This is in contrast to human genetics that use of linkage disequilibrium (LD)-based mapping for fine mapping of QTLs using single nucleotide polymorphisms. LD based association mapping (AM) has promise to be used in plants. Possible use of such approach may be for fine mapping of genes / QTLs, identifying favorable alleles for marker aided selection and cross validation of results from linkage mapping for precise location of genes / QTLs of interest. In the present review, we discuss different mapping populations, approaches, prospects and limitations of using association mapping in plant breeding populations. This is expected to create awareness in plant breeders in use of AM in crop improvement activities.Key words: Association mapping; plant breeding; DNA marker; quantitative trait lociDOI: http://dx.doi.org/10.3126/njb.v2i1.5686 Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 72-89

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Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

10.21203/rs.3.rs-779119/v1 ◽

2021 ◽

Author(s):

Guai-qiang Chai ◽

Yizhong Duan ◽

Peipei Jiao ◽

Zhongyu Du ◽

Furen Kang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Association Studies ◽

Natural Populations ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Future Design ◽

Ammopiptanthus Nanus ◽

Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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