Evolutionary Subdivision of Domestic Chickens: Implications for Local Breeds as Assessed by Phenotype and Genotype in Comparison to Commercial and Fancy Breeds

To adjust breeding programs for local, commercial, and fancy breeds, and to implement molecular (marker-assisted) breeding, a proper comprehension of phenotypic and genotypic variation is a sine qua non for breeding progress in animal production. Here, we investigated an evolutionary subdivision of domestic chickens based on their phenotypic and genotypic variability using a wide sample of 49 different breeds/populations. These represent a significant proportion of the global chicken gene pool and all major purposes of breed use (according to their traditional classification model), with many of them being characterized by a synthetic genetic structure and notable admixture. We assessed their phenotypic variability in terms of body weight, body measurements, and egg production. From this, we proposed a phenotypic clustering model (PCM) including six evolutionary lineages of breed formation: egg-type, meat-type, dual purpose (egg-meat and meat-egg), game, fancy, and Bantam. Estimation of genotypic variability was carried out using the analysis of five SNPs, i.e., at the level of genomic variation at the NCAPG-LCORL locus. Based on these data, two generally similar genotypic clustering models (GCM1 and GCM2) were inferred that also had several overlaps with PCM. Further research for SNPs associated with economically important traits can be instrumental in marker-assisted breeding programs.

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Spikelet abortion in six-rowed barley is mainly influenced by final spikelet number with potential spikelet number acting as a suppressor trait

Journal of Experimental Botany ◽

10.1093/jxb/erab529 ◽

2021 ◽

Author(s):

Roop Kamal ◽

Quddoos H Muqaddasi ◽

Yusheng Zhao ◽

Thorsten Schnurbusch

Keyword(s):

Grain Yield ◽

Phenotypic Variability ◽

Genotypic Variation ◽

Maximum Yield ◽

Barley Grain ◽

Yield Potential ◽

Large Set ◽

Spikelet Number ◽

Phenotypic Data ◽

Pass Through

Abstract The potential to increase barley grain yield lies in the indeterminate nature of its inflorescence meristem (IM). The IM produces spikelets, the basic reproductive unit in grasses, which are linked to reproductive success. During early reproductive growth, barley spikes pass through the maximum yield potential—a stage after which no new spikelet ridges are produced. Subsequently, spikelet abortion (SA), a phenomenon in which spikelets abort during spike growth, imposes a bottleneck on increasing the grain yield potential. Here, we studied the potential of main culm spikes by counting potential spikelet number (PSN), final spikelet number (FSN) and computed the corresponding SA (%) in a panel of 417 six-rowed spring barleys. Our phenotypic data analyses showed a significantly large within- and across-years genotypic variation with high broad-sense heritability estimates for all the investigated traits, including SA. Asian accessions displayed the lowest SA indicating the presence of favorable alleles that may be exploited in breeding programs. A significantly negative Pearson’s product-moment correlation was observed between FSN and SA. Our path analysis revealed that PSN and FSN explain 93% of the observed phenotypic variability for SA with PSN behaving as a suppressor trait magnifying the effect. Based on a large set of diverse barley accessions, our results provide a deeper phenotypic understanding of the quantitative genetic nature of SA, its association with traits of high agronomic importance, and a resource for further genetic analyses.

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Short communication: QTL mapping for ear tip-barrenness in maize

Spanish Journal of Agricultural Research ◽

10.5424/sjar/2016143-9325 ◽

2016 ◽

Vol 14 (3) ◽

pp. e07SC01 ◽

Cited By ~ 1

Author(s):

Junqiang Ding ◽

Jinliang Ma ◽

Jiafa Chen ◽

Tangshun Ai ◽

Zhimin Li ◽

...

Keyword(s):

Quantitative Trait ◽

Genetic Basis ◽

Mixed Model ◽

Short Communication ◽

Genotypic Variation ◽

Interval Mapping ◽

Mapping Method ◽

Additive Effects ◽

Breeding Programs ◽

Model Composite

Barren tip on corn ear is an important agronomic trait in maize, which is highly associated with grain yield. Understanding the genetic basis of tip-barrenness may help to reduce the ear tip-barrenness in breeding programs. In this study, ear tip-barrenness was evaluated in two environments in a F2:3 population, and it showed significant genotypic variation for ear tip-barrenness in both environments. Using mixed-model composite interval mapping method, three additive effects quantitative trait loci (QTL) for ear tip-barrenness were mapped on chromosomes 2, 3 and 6, respectively. They explained 16.6% of the phenotypic variation, and no significant QTL × Environment interactions and digenic interactions were detected. The results indicated that additive effect was the main genetic basis for ear tip-barrenness in maize. This is the first report of QTL mapped for ear tip-barrenness in maize.

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Use of water extraction variability to screen for sunflower genotypes well adapted to soil water limitation

Functional Plant Biology ◽

10.1071/fp11235 ◽

2012 ◽

Vol 39 (12) ◽

pp. 999

Author(s):

Ando M. Radanielson ◽

Jeremie Lecoeur ◽

Angelique Christophe ◽

Lydie Guilioni

Keyword(s):

Soil Water ◽

Phenotypic Variability ◽

Water Extraction ◽

Breeding Programs ◽

Mean Values ◽

Relative Value ◽

Water Uptake Capacity ◽

Extraction Properties ◽

Soil Water Extraction ◽

The Mean

In conditions of water deficit, plant yield depends mostly on the ability of the plant to explore soil profile and its water uptake capacity per unit volume of soil. In this study, the value of soil water extraction properties for use in sunflower breeding was evaluated. Five experiments were carried out in pots, in greenhouses, from 2005 to 2009, in Montpellier, France. Elite sunflower cultivars and experimental hybrids obtained from a factorial cross between five female and five male inbred lines were grown. The soil water extraction performance of the plants was characterised by the soil water content at minimal stomatal conductance (SWCgs = 0) and the index of water extraction (IEgen), which was calculated as the relative value of SWCgs = 0 to the performance of the cultivar NKMelody. Heritability (H2) was estimated for the experimental hybrids. Phenotypic variability of the SWCgs = 0 was observed with a significant effect of the environment and the genotype. The latest released cultivars were observed as the best performing one in water extraction with an IEgen under 0.85. This trait was found to be suitable for use in comparisons of the soil water extraction performances of different genotypes. The high H2 value for SWCgs = 0 (0.77 and 0.81) and the significant correlation (r2 = 0.70, P < 0.001) between the values obtained for the experimental hybrids and the mean values of the general combining ability (GCA) for the parental lines showed that this trait is heritable and could be used in plant breeding programs. Phenotyping methods and the usefulness of this trait in crop modelling are discussed.

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FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data

Briefings in Bioinformatics ◽

10.1093/bib/bbz117 ◽

2019 ◽

Vol 21 (5) ◽

pp. 1837-1845

Author(s):

Ephifania Geza ◽

Nicola J Mulder ◽

Emile R Chimusa ◽

Gaston K Mazandu

Keyword(s):

Phenotypic Variability ◽

Modern Human ◽

Genomic Variation ◽

Unified Framework ◽

Local Ancestry ◽

Human Heredity ◽

Snp Data ◽

Variation Patterns ◽

Adaptive Processes ◽

Local Ancestry Inference

Abstract Several thousand genomes have been completed with millions of variants identified in the human deoxyribonucleic acid sequences. These genomic variations, especially those introduced by admixture, significantly contribute to a remarkable phenotypic variability with medical and/or evolutionary implications. Elucidating local ancestry estimates is necessary for a better understanding of genomic variation patterns throughout modern human evolution and adaptive processes, and consequences in human heredity and health. However, existing local ancestry deconvolution tools are accessible as individual scripts, each requiring input and producing output in its own complex format. This limits the user’s ability to retrieve local ancestry estimates. We introduce a unified framework for multi-way local ancestry inference, FRANC, integrating eight existing state-of-the-art local ancestry deconvolution tools. FRANC is an adaptable, expandable and portable tool that manipulates tool-specific inputs, deconvolutes ancestry and standardizes tool-specific results. To facilitate both medical and population genetics studies, FRANC requires convenient and easy to manipulate input files and allows users to choose output formats to ease their use in further potential local ancestry deconvolution applications.

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Morpho-agronomic characterization and estimates of genetic parameters in annatto plant

Horticultura Brasileira ◽

10.1590/s0102-053620170214 ◽

2017 ◽

Vol 35 (2) ◽

pp. 242-246 ◽

Cited By ~ 1

Author(s):

Nilma O Dias ◽

Tiyoko NH Rebouças ◽

Abel R São José ◽

Cláudio LF Amaral

Keyword(s):

Genetic Parameters ◽

Environmental Influence ◽

Genotypic Variation ◽

Morphological Characterization ◽

Breeding Programs ◽

Tropical America ◽

Self Fertilization ◽

Superior Genotypes ◽

Increasing Demand

ABSTRACT Originally from tropical America, annatto is an important source of natural dyes for food, pharmaceutical and textile industries, especially for the increasing demand of this pigment substituting artificial dyes. The aim of this study was to evaluate genotypic variation of annatto cultivar Embrapa 37, aiming to generate subsidies for breeding programs as well as to help out the producers using vegetative propagation of superior genotypes. Therefore, the morphological characterization was carried out and estimates of genetic and phenotypic parameters, for production and quality of the fruits, were obtained. The results showed wide rate of genetic variability among the plants with low environmental influence on the phenotype for traits bixin content, fruit width, number of fruits per bunch and mass of 100 seeds. The authors concluded that superior genotypes can be selected through the parental performance and propagated vegetatively to form more profitable crops, as well as used in breeding programs through self-fertilization with analysis of resulting progeny.

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Genotypic and Phenotypic Variability for Yield and its Components in Normal and Late Sown Chickpea (Cicer arietinum L.)

Legume Research - An International Journal ◽

10.18805/lr-505 ◽

2019 ◽

Author(s):

D Yücel

Keyword(s):

Cicer Arietinum ◽

Phenotypic Variability ◽

Block Design ◽

Climatic Conditions ◽

High Yield ◽

Breeding Programs ◽

Cicer Arietinum L ◽

Drought Tolerant ◽

Coefficients Of Variation ◽

Late Sowing

Chickpea (Cicer arietinum L.) is one of the important legumes widely grown for dietary proteins in semi-arid Mediterranean climatic conditions. The main goal of any breeding programs in the world is to produce high yield and better quality genotypes for farmers and commercial growers to be released as cultivars. Present research has been conducted to select more desirable characteristics that may contribute to the improvement of drought tolerant chickpea. Thirty-two chickpea genotypes along with two control varieties were evaluated in winter and late sowing conditions in 2015 and 2016, in randomized complete block design with three replications. Phenotypic coefficients of variation were found to be higher than genotypic coefficients of variation for all the traits. The highest heritability along with high genetic advance was found for hundred seed weight followed by podding day, plant height, flowering day and first pod height in normal and stress conditions. These traits can be improved by giving special attention during selection.

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Australian canola germplasm differs in nitrogen and sulfur efficiency

Australian Journal of Agricultural Research ◽

10.1071/ar06255 ◽

2008 ◽

Vol 59 (2) ◽

pp. 167 ◽

Cited By ~ 13

Author(s):

Tatjana Balint ◽

Zdenko Rengel ◽

David Allen

Keyword(s):

Genotypic Variation ◽

Dry Weight ◽

Breeding Programs ◽

Relative Growth ◽

Breeding Lines ◽

Shoot Dry Weight ◽

Sulfur Supply ◽

Utilisation Efficiency ◽

Low Sulfur ◽

Low Nitrogen

Eighty-four canola genotypes, including current commercial Australian genotypes, some older Australian genotypes, new breeding lines, and several genotypes from China, were screened for nitrogen and sulfur efficiency in the early growth stage. Plants were grown in a glasshouse using virgin brown Lancelin soil (Uc4.22) supplied with basal nutrients. The treatments were: (i) adequate nitrogen and sulfur, (ii) low nitrogen, and (iii) low sulfur. Canola shoots were harvested at 38 days after sowing when growth reduction and the nitrogen and sulfur deficiency symptoms were evident in most genotypes. The nitrogen or sulfur efficiency in canola genotypes was evaluated on the basis of: (1) growth at low nitrogen or sulfur supply, (2) growth at low relative to adequate nitrogen and sulfur supply, and (3) nitrogen or sulfur utilisation efficiency expressed as shoot dry weight per unit of nitrogen or sulfur content in shoots. Genotypic variation in growth and nitrogen or sulfur efficiency in canola germplasm was significant. Two genotypes (Chikuzen and 46C74) were ranked efficient and 2 inefficient (CBWA-005 and Beacon) in uptake and utilisation of nitrogen under all 3 criteria. In terms of sulfur efficiency, genotype Argentina was ranked efficient, whereas CBWA-003 and IB 1363 were classified inefficient under all 3 criteria. Two canola genotypes (Surpass 600 and 46C74) were both nitrogen- and sulfur-efficient in terms of relative growth at low v. adequate nutrition; their use in the breeding programs could be considered.

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Phenotypic variability of cowpea genotypes for immature seed harvesting

Pesquisa Agropecuária Tropical ◽

10.1590/1983-40632021v5169614 ◽

2021 ◽

Vol 51 ◽

Author(s):

Deisy Aiane Lima de Aquino ◽

Carlos Antônio Fernandes Santos ◽

Danillo Olegário Matos da Silva

Keyword(s):

Growth Habit ◽

Phenotypic Variability ◽

Immature Seed ◽

Jaccard Coefficient ◽

Seed Color ◽

Clustering Methods ◽

Breeding Programs ◽

Plant Growth Habit ◽

Immature Seeds ◽

Seed Harvesting

ABSTRACT Seed color, brightness and texture are important aspects for the consumption of immature beans. This study aimed to estimate the phenotypic variability among thirty cowpea genotypes for immature seed harvesting, in order to guide breeding programs. The experiment was carried out in a randomized blocks design, with three replications. The evaluated traits were immature seeds yield, pods and dry seeds production, number of immature pods, 100-immature seeds weight, immature pods length, number of seeds per immature pod, cooking time, harvesting period of immature pods, seed color, pod color, plant growth habit, opening of immature pods, seed threshing from immature pods, cultivation value and seed browning after threshing. Anova and three clustering methods were applied: UPGMA using the Jaccard coefficient of similarity; modified Tocher method based on the Gower algorithm; and k-means. All the analyses were performed based on the variable means of experiments evaluated in six environments. A statistically significant phenotypic variability was observed among all the quantitative traits. Discrepancies occurred in the accessions grouping and number of clusters. The accession BRS Acauã, in one group, and P508 and PCCR3F6L15, in other groups, showed a good quality for immature grain harvesting, were consistently grouped into different clusters and are recommended for use as parents in the development of new cultivars.

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The Rhizosphere Bacterial Communities Differ Among Domesticated Maize Landraces – An Experimental Confirmation

10.1101/2021.12.30.474574 ◽

2022 ◽

Author(s):

Mads Lund ◽

Jacob Agerbo Rasmussen ◽

Jazmin Ramos-Madrigal ◽

M. Thomas Pius Gilbert ◽

Christopher James Barnes

Keyword(s):

Bacterial Communities ◽

Environmental Gradients ◽

Genotypic Variation ◽

Single Species ◽

Genomic Variation ◽

Genotypic Differences ◽

Limited Sampling ◽

Maize Landraces ◽

Controlled Environments ◽

Rhizosphere Bacterial Communities

The plant-associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results often confounded by the larger effects of climatic and edaphic variation. In this study, the effect of genomic variation on the rhizosphere bacterial communities of maize was investigated by comparing different genotypes grown within controlled environments. Rhizosphere bacterial communities were profiled by metabarcoding the universal bacterial 16S rRNA v3-v4 region. Initially, plants from the inbred B73 line and the Ancho - More 10 landrace were grown for 12-weeks and compared. The experiment was then repeated with an additional four Mexican landraces (Apachito - Chih 172, Tehua - Chis 204, Serrano - Pueb 180 and Hairnoso de Ocho) that were grown alongside additional B73 and Ancho - More 10 genotypes. In both experiments there were significant genotypic differences in the rhizosphere bacteria. Additionally, the bacterial communities were significantly correlated with genomic distance between genotypes, with the more closely related landraces being more similar in rhizosphere bacterial communities. Despite limited sampling numbers, here we confirm that genomic variation in maize landraces is associated with differences in the rhizosphere bacterial communities. Further studies that go beyond correlations to identify the mechanisms that determine the genotypic variation of the rhizosphere microbiome are required.

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Marker-assisted breeding of onion (A. cepa L.) maintainer line resistant to Downy mildew

VEGETABLE CROPS OF RUSSIA ◽

10.18619/2072-9146-2021-3-34-39 ◽

2021 ◽

pp. 34-39

Author(s):

Ya. T. Eidlin ◽

G. F. Monakhos ◽

S. G. Monakhos

Keyword(s):

Downy Mildew ◽

Inbred Line ◽

Marker Assisted Selection ◽

Dna Marker ◽

F1 Hybrids ◽

Marker Assisted Breeding ◽

Maintainer Line ◽

Breeding Programs ◽

Maternal Line ◽

Two Generations

Relevance. F1 hybrids breeding programs of onion are based on the use of nuclear cytoplasmic male sterility (NCMS). Breeding and seed production based on NCMS suggest a development of a female sterile maternal line, a maintainer line and a paternal component. The development of an isogenic pair of sterile line – maintainer line is one of the most labor-, time-consuming and intellectually-intensive stages of a breeding program, the implementation of which becomes more complicated with an increase in the number of traits / genes for which selection is carried out.Methods and results. This paper presents a genetic scheme for the development of a Downy mildewresistant (pathogen P. destructor) maintainer line of onion using marker-assisted selection (MAS). F2 populations were obtained from the cross of the female maintainer inbred line, Bn1- (13) (genotype – cytN msms pdpd) and male inbred line resistant to Downy mildew, No. 136 (genotype – cytT MsMs PdPd). DNA marker DMR1 were used for Downy mildew resistance gene Pd, jnurf13 – for maintainer gene ms and marker system 5`cob: orfA501 – for N, S and T cytoplasms. It was shown that the MAS application allow to develop a stable Downy mildew resistant maintainer line cytN msms PdPd in two generations.

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