scholarly journals Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Noah DeWitt ◽  
Mohammed Guedira ◽  
Edwin Lauer ◽  
J. Paul Murphy ◽  
David Marshall ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Plant Growth ◽  
Genomic Selection ◽  
Plant Height ◽  
Prediction Models ◽  
Growth Traits ◽  
Heading Date ◽  
Additive Genetic Variation ◽  
Moderate Effect ◽  
Over Time

Abstract Background Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL. Results We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models. Conclusions In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.

scholarly journals 211 Changes in genetic parameters of fitness and growth traits under genomic selection in pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 41-41
Author(s):  
Jorge Hidalgo ◽  
Shogo Tsuruta ◽  
Daniela Lourenco ◽  
Yijian Huang ◽  
Kent Gray ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genomic Selection ◽  
Variance Components ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Data Set ◽  
Daily Gain ◽  
Over Time

Abstract Genomic selection increases intensity of selection and decreases generation interval. However, intensive selection reduces genetic variation and can strengthen undesirable genetic correlations. The purpose of this study was to investigate changes in genetic parameters of litter size (LS), number born alive (NBA), number born dead (NBD) and average daily gain (ADG) and weight at off-test (WT) in pigs over time. The data set contained 20,086 (LS), 21,230 (NBA), 21,230 (NBD), 144,717 (ADG) and 144,718 (WT) phenotypic records. Pedigree file included 369,776 animals born between 2001 and 2018, of which 39,038 were genotyped. Two trait models were evaluated (LS-ADG, LS-WT, NBA-ADG, NBA-WT, NBD-ADG and NBD-WT) using 3-year sliding subsets starting from 2010. Variance components and genetic parameters were estimated using GIBBS2F90 program. Computations were performed with (BLUP) or without (ssGBLUP) genotypes. For BLUP (ssGBLUP), the changes in heritability from 2010–2012 to 2015–2018 were 0.08 to 0.09 (0.08 to 0.06) for LS, 0.33 to 0.24 (0.37 to 0.16) for ADG, 0.11 to 0.07 (0.10 to 0.07) for NBD, and 0.32 to 0.24 (0.38 to 0.17) for WT. Differences were also observed for genetic correlations as they were -0.23 to -0.73 (-0.31 to -0.58) for LS-ADG, -0.24 to -0.74 (-0.31 to -0.50) for LS-WT, -0.33 to -0.65 (-0.41 to -0.53) for NBA-ADG, -0.35 to -0.66 (-0.42 to -0.45) for NBA-WT, 0.12 to 0.04 (0.12 to 0.16) for NBD-ADG, and 0.11 to 0.05 (0.11 to 0.22) for NBD-WT. Genomic selection in pigs reduced heritabilities and emphasized the antagonistic relationship that are under strong selection. Heritabilities estimated from ssGBLUP declined more than those by BLUP while changes in the genetic correlations were smaller and more gradual by ssGBLUP. Differences between ssGBLUP and BLUP could be caused by genomic pre-selection unaccounted for by BLUP.

scholarly journals Genomic Selection in Winter Wheat Breeding Using a Recommender Approach

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 779
Author(s):  
Dennis N. Lozada ◽  
Arron H. Carter
Keyword(s):  
Winter Wheat ◽  
Genomic Selection ◽  
Prediction Models ◽  
Heading Date ◽  
Predictive Ability ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Bayesian Regression ◽  
Phenotypic Trait ◽  
Breeding Programs

Achieving optimal predictive ability is key to increasing the relevance of implementing genomic selection (GS) approaches in plant breeding programs. The potential of an item-based collaborative filtering (IBCF) recommender system in the context of multi-trait, multi-environment GS has been explored. Different GS scenarios for IBCF were evaluated for a diverse population of winter wheat lines adapted to the Pacific Northwest region of the US. Predictions across years through cross-validations resulted in improved predictive ability when there is a high correlation between environments. Using multiple spectral traits collected from high-throughput phenotyping resulted in better GS accuracies for grain yield (GY) compared to using only single traits for predictions. Trait adjustments through various Bayesian regression models using genomic information from SNP markers was the most effective in achieving improved accuracies for GY, heading date, and plant height among the GS scenarios evaluated. Bayesian LASSO had the highest predictive ability compared to other models for phenotypic trait adjustments. IBCF gave competitive accuracies compared to a genomic best linear unbiased predictor (GBLUP) model for predicting different traits. Overall, an IBCF approach could be used as an alternative to traditional prediction models for important target traits in wheat breeding programs.

scholarly journals Genetic Variation Among and Within Populations in Swedish Species of Sorbus aucuparia L. and Prunus padus L. Assessed in a Nursery Trial

2005 ◽  
Vol 54 (1-6) ◽  
pp. 1-8 ◽  
Author(s):  
V. Baliuckas ◽  
T. Lagerström ◽  
L. Norell ◽  
G. Eriksson
Keyword(s):  
Genetic Variation ◽  
Growth Traits ◽  
Genetic Correlations ◽  
Population Variation ◽  
Sorbus Aucuparia ◽  
Population Effect ◽  
Prunus Padus ◽  
Bud Flushing ◽  
Over Time ◽  
Leaf Colouring

Abstract Seedlings originating from open-pollinated offspring of six and four populations of Prunus padus and Sorbus aucuparia, respectively, were studied with respect to phenology and growth traits for 3-4 years in a nursery. There were no replications at the population levels since the experiments should be converted to seedling seed orchards. Therefore, a special statistical model for analysis of the population effect was developed making use of neighbour performances. This model was also used for derivation of heritabilities. The heritabilities for phenology traits were in many cases high in P. padus, > 0.40, while they varied in the range 0.07-0.62 in S. aucuparia. The population effect was significant for all growth rhythm traits in P. padus and for a majority of traits in S. aucuparia. In both species the heritability for height decreased over time. Only bud flushing in P. padus indicated a relationship with population latitudinal origin in some cases. The genetic correlations between bud flushing different years were relatively strong in both species while the corresponding correlations for leaf colouring were moderate in P. padus and weak in S. aucuparia. In conclusion, the observed structure suggests that the pattern of seed dispersal may have an influence on the among- and within-population variation.

GENETIC VARIATION OF FOUR TRAITS IN A POPULATION OF ZIZANIA AQUATICA

1980 ◽  
Vol 60 (1) ◽  
pp. 1-4 ◽  
Author(s):  
K. W. FOSTER ◽  
J. N. RUTGER
Keyword(s):  
Genetic Variation ◽  
Plant Height ◽  
Random Sample ◽  
Wild Rice ◽  
Heading Date ◽  
Tiller Number ◽  
Seed Length ◽  
Additive Variance ◽  
Phenotypic Correlations ◽  
Zizania Aquatica

Genetic variation for four characters in a population of wild rice (Zizania aquatica L.) was investigated using a random sample of 100 open-pollinated progenies grown in a single environment. Additive variance was present in significant amounts for heading date, plant height, tiller number, and seed length. Expected gains from selection were substantial for all traits. All phenotypic correlations among the four characters were significant, except for the correlation of plant height with seed length. Thus, correlated selection responses are possible.

Comparing Genetic Variation within Red Winter Wheat Populations with and without Image-Based Optical Sorter Selection

2019 ◽  
Vol 9 (2) ◽  
pp. 266-277
Author(s):  
Hussein M. Khaeim ◽  
Anthony Clark ◽  
Tom Pearson ◽  
Dr. David Van Sanford
Keyword(s):  
Genetic Variation ◽  
Fusarium Head Blight ◽  
Heading Date ◽  
Fusarium Head Blight Resistance ◽  
Gibberella Zeae ◽  
Mass Selection ◽  
Head Blight ◽  
Red Winter Wheat ◽  
Two Populations ◽  
Head Scab

Head scab is historically a devastating disease affecting not just all classes of wheat but also barley and other small grains around the world. Fusarium head blight (FHB), or head scab, is caused most often by Fusarium graminearum (Schwabe), (sexual stage – Gibberella zeae) although several Fusarium spp. can cause the disease. This study was conducted to determine the effect of mass selection for FHB resistance using an image-based optical sorter. lines were derived from the C0 and C2 of two populations to compare genetic variation within populations with and without sorter selection. Our overall hypothesis is that sorting grain results in improved Fusarium head blight resistance. Both of the used wheat derived line populations have genetic variation, and population 1 has more than population 17. They are significantly different from each other for fusarium damged kernel (FDK), deoxynivalenol (DON), and other FHB traits. Although both populations are suitable to be grown for bulks, population 1 seems better since it has more genetic variation as well as lower FDK and DON, and earlier heading date. Lines within each population were significantly different and some lines in each population had significantly lower FDK and DON after selection using an optical sorter. Some lines had significant reduction in both FDK and DON, and some others had either FDK or DON reduction. Lines of population 1 that had significant reduction, were more numerous than in population 17, and FDK and DON reduction were greater.

QTL Analysis for Plant Height and Heading Date in Rice under Two Nitrogen Levels

2011 ◽  
Vol 37 (9) ◽  
pp. 1525-1532 ◽  
Author(s):  
Yue FENG ◽  
Rong-Rong ZHAI ◽  
Li-Yong CAO ◽  
Ze-Chuan LIN ◽  
Xing-Hua WEI ◽  
...  
Keyword(s):  
Plant Height ◽  
Qtl Analysis ◽  
Heading Date ◽  
Nitrogen Levels

Film coating of seeds with Bacillus cereus RS87 spores for early plant growth enhancement

2008 ◽  
Vol 54 (10) ◽  
pp. 861-867 ◽  
Author(s):  
Kanchalee Jetiyanon ◽  
Sakchai Wittaya-Areekul ◽  
Pinyupa Plianbangchang
Keyword(s):  
Plant Growth ◽  
Bacillus Cereus ◽  
Plant Height ◽  
Root Length ◽  
Film Coating ◽  
Field Trials ◽  
Growth Enhancement ◽  
Vegetative Cells ◽  
Plant Growth Promoting ◽  
Growth Promoting

The plant growth-promoting rhizobacterium Bacillus cereus RS87 was previously reported to promote plant growth in various crops in both greenhouse and field trials. To apply as a plant growth promoting agent with practical use, it is essential to ease the burden of routine preparation of a fresh suspension of strain RS87 in laboratory. The objectives of this study were to investigate the feasibility of film-coating seeds with B. cereus RS87 spores for early plant growth enhancement and to reveal the indoleacetic acid (IAA) production released from strain RS87. The experiment consisted of the following 5 treatments: nontreated seeds, water-soaked seeds, film-coated seeds, seeds soaked with vegetative cells of strain RS87, and film-coated seeds with strain RS87 spores. Three experiments were conducted separately to assess seed emergence, root length, and plant height. Results showed that both vegetative cells and spores of strain RS87 significantly promoted (P ≤ 0.05) seed emergence, root length and plant height over the control treatments. The strain RS87 also produced IAA. In conclusion, the film coating of seeds with spores of B. cereus RS87 demonstrated early plant growth enhancement as well as seeds using their vegetative cells. IAA released from strain RS87 would be one of the mechanisms for plant growth enhancement.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals Musik Gamelan Bali Meningkatkan Pertumbuhan dan Produktivitas Tanaman Sawi Pakcoy (Brassica rafa L.)

2018 ◽  
Vol 6 (2) ◽  
pp. 73
Author(s):  
Dewa Putu Yoga Gautama ◽  
I Made Anom S. Wijaya ◽  
I Wayan Widia
Keyword(s):  
Plant Growth ◽  
Plant Height ◽  
High Frequency ◽  
Dry Weight ◽  
Sound Waves ◽  
High Frequency Sound ◽  
Frequency Sound ◽  
Green Leaves ◽  
Mustard Plant ◽  
Canopy Area

Pemberian gelombang suara dengan frekuensi tinggi dapat merangsang mulut daun  (stomata) tetap terbuka, akibatnya laju dan efisiensi penyerapan pupuk meningkat yang bermanfaat bagi tanaman. Hasil penggunaan sonic bloom pada tanaman adalah mampu menstimulir metabolisme sel-sel tanaman, sehingga terjadi peningkatan penyerapan nutrisi dan uap air lewat daun yang berpengaruh pada pertumbuhan dan produktivitas tanaman. Tujuan dari penelitian ini yaitu (1) untuk mengetahui pengaruh pemberian musik Gamelan Bali terhadap pertumbuhan dan produktivitas tanaman sawi pakcoy dan (2) untuk menentukan jenis musik Gamelan Bali yang memberikan pertumbuhan dan produktivitas sawi pakcoy yang terbaik. Penelitan ini menggunakan tanaman sawi pakcoy (Brassica Rafa L.).  Perlakuan yang diberikan  dalam penelitian adalah pemberian musik gamelan bali dengan nuansa musik yang berbeda. Perlakuan 1 menggunakan musik gamelan Angklung, Perlakuan 2 menggunakan musik gamelan Semarpagulingan dan Perlakuan 3 menggunakan musik gamelan Gong Kebyar. Data yang diperoleh dianalis ANOVA dengan program IBM SPSS 20. Variabel yang diamati yaitu tinggi tanaman, luas kanopi daun tanaman, tingkat kehijauan daun tanaman, dan berat kering. Hasil penelitian menunjukan bahwa pemberian musik gong kebyar menghasilkan nilai tertinggi pada variabel tinggi tanaman, luas kanopi daun, tingkat kehijauan daun, dan berat kering yang  masing menghasilkan nilai yaitu yaitu 29,98 cm, 1684 cm2, 186,79, dan 68,61 gr. Pemberian musik memberikan pengaruh yang positif dan berbeda nyata pada pertumbuhan tanaman sawi pakcoy. Semakin tinggi frekuensi musik yang diberikan maka semakin baik pertumbuhan tanaman sawi pakcoy yang dihasilkan.  High frequency sound waves can stimulate the mouth of leaf (stomata) remains opened.The stomata remains open leading to efficient absorption of fertilizer. The purposes of this research were (1) to find out the effect of Balinese instrument music on the growth and productivity of pakcoy mustard plant and (2) to determine the type of Balinese instrument music that gives the best growth and productivity of mustard pakcoy. The treatment of this research was the application of Balinese instrument music with different musical nuances for 3 hours. Treatment 1 was using Angklung instruments music, treatment 2 was using Semarpagulingan instrument music and treatment 3 using Gong Kebyar instrument music. The obtained data was analized by ANOVA with the IBM SPSS 20 program. The observed variables include plant height, canopy area of plant leaf, green leaves level and dry weight. The results showed that Gong Kebyar instrument music application produces the highest value of 29.98 on the height of the plant variables, the widest value of 1684 cm2  on the canopy area variables, the biggest value that is 68,61 gr on the dry weight variables and the largest value of 186.79 on the green leaves level variables. Balinese instrument music application effect to the growth of pakcoy mustard plant. The best plant growth was the plant with gong kebyar instrument music application from all observed variables.

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