scholarly journals Development of Optimized Phenomic Predictors for Efficient Plant Breeding Decisions Using Phenomic-Assisted Selection in Soybean

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Kyle Parmley ◽  
Koushik Nagasubramanian ◽  
Soumik Sarkar ◽  
Baskar Ganapathysubramanian ◽  
Asheesh K. Singh
Keyword(s):  
Seed Yield ◽  
Optimization Techniques ◽  
Phenotypic Traits ◽  
Yield Data ◽  
Crop Species ◽  
Breeding Programs ◽  
High Throughput Phenotyping ◽  
Complex Relationships ◽  
Sensor Package ◽  
Made In

The rate of advancement made in phenomic-assisted breeding methodologies has lagged those of genomic-assisted techniques, which is now a critical component of mainstream cultivar development pipelines. However, advancements made in phenotyping technologies have empowered plant scientists with affordable high-dimensional datasets to optimize the operational efficiencies of breeding programs. Phenomic and seed yield data was collected across six environments for a panel of 292 soybean accessions with varying genetic improvements. Random forest, a machine learning (ML) algorithm, was used to map complex relationships between phenomic traits and seed yield and prediction performance assessed using two cross-validation (CV) scenarios consistent with breeding challenges. To develop a prescriptive sensor package for future high-throughput phenotyping deployment to meet breeding objectives, feature importance in tandem with a genetic algorithm (GA) technique allowed selection of a subset of phenotypic traits, specifically optimal wavebands. The results illuminated the capability of fusing ML and optimization techniques to identify a suite of in-season phenomic traits that will allow breeding programs to decrease the dependence on resource-intensive end-season phenotyping (e.g., seed yield harvest). While we illustrate with soybean, this study establishes a template for deploying multitrait phenomic prediction that is easily amendable to any crop species and any breeding objective.

scholarly journals Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Siles ◽  
Kirsty L. Hassall ◽  
Cristina Sanchis Gritsch ◽  
Peter J. Eastmond ◽  
Smita Kurup
Keyword(s):  
Oilseed Rape ◽  
Seed Yield ◽  
Complex Trait ◽  
Growth Conditions ◽  
Phenotypic Traits ◽  
Oilseed Crop ◽  
Crop Species ◽  
Trade Offs ◽  
Whole Plant ◽  
Plant Level

Seed yield is a complex trait for many crop species including oilseed rape (OSR) (Brassica napus), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions, or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, how female reproductive traits contribute to whole plant level traits, and hence to seed yield, has been largely ignored. Here, we describe the combined contribution of 33 phenotypic traits within a B. napus diversity set population and their trade-offs at the whole plant and organ level, along with their interaction with plant level traits. Our results revealed that both Winter OSR (WOSR) and Spring OSR (SOSR); the two more economically important OSR groups in terms of oil production; share a common dominant reproductive strategy for seed yield. In this strategy, the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. Moreover, we observed that WOSR opted for additional reproductive strategies than SOSR, presenting more plasticity to maximise seed yield. Overall, we conclude that OSR adopts a key strategy to ensure maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding.

Short Communication: Comparative effect of lodging on seed yield of flax and wheat

2012 ◽  
Vol 92 (1) ◽  
pp. 39-43 ◽  
Author(s):  
C. L. Vera ◽  
S. D. Duguid ◽  
S. L. Fox ◽  
K. Y. Rashid ◽  
J. C. P. Dribnenki ◽  
...  
Keyword(s):  
Seed Yield ◽  
Short Communication ◽  
Severe Disease ◽  
Triticum Aestivum L ◽  
Crop Productivity ◽  
Comparative Effect ◽  
Yield Data ◽  
Crop Species ◽  
Breeding Lines ◽  
Linum Usitatissimum L

Vera, C. L., Duguid, S. D., Fox, S. L., Rashid, K. Y., Dribnenki, J. C. P. and Clarke, F. R. 2012. Short Communication: Comparative effect of lodging on seed yield of flax and wheat. Can. J. Plant Sci. 92: 39–43. Lodging may limit crop productivity and hinder the normal process of harvesting crops. Results from 16 yr (1994–2009) of the Flax Co-operative test and from 29 yr (1981–2009) of the Central Bread Wheat Co-operative test, conducted annually for the evaluation of advanced breeding lines at various locations in the provinces of Manitoba, Saskatchewan and Alberta, Canada, were used to determine the effect of lodging on the seed yield of these two crop species. Seed yield data were regressed on corresponding lodging scores (1–9 scale) collected from field evaluations. Lodging was more frequently a problem in flax (Linum usitatissimum L.) than in wheat (Triticum aestivum L.), with average seed yield reductions of 32% and 16%, respectively, when lodging was most severe. Disease has been observed in association with the occurrence of lodging in flax. Further research is necessary to elucidate the participation of airborne and soil microorganisms, particularly pasmo, caused by Septoria linicola (Speg.) Garassini, in the mode and degree to which flax is subjected to, and affected by, lodging.

Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

Genome ◽  
2007 ◽  
Vol 50 (4) ◽  
pp. 373-384 ◽  
Author(s):  
M. Maccaferri ◽  
S. Stefanelli ◽  
F. Rotondo ◽  
R. Tuberosa ◽  
M.C. Sanguineti
Keyword(s):  
Durum Wheat ◽  
Genetic Relatedness ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Pedigree Data ◽  
Crop Species ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Triticum Durum Desf

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders’ rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat ( Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

scholarly journals Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Delphine M. Pott ◽  
Sara Durán-Soria ◽  
Sonia Osorio ◽  
José G. Vallarino
Keyword(s):  
Quality Trait ◽  
Quality Traits ◽  
Crop Species ◽  
Breeding Programs ◽  
Crop Quality ◽  
Crop Varieties ◽  
New Genes ◽  
Technical Advances ◽  
Health Promoting ◽  
Selection Of

AbstractPlant quality trait improvement has become a global necessity due to the world overpopulation. In particular, producing crop species with enhanced nutrients and health-promoting compounds is one of the main aims of current breeding programs. However, breeders traditionally focused on characteristics such as yield or pest resistance, while breeding for crop quality, which largely depends on the presence and accumulation of highly valuable metabolites in the plant edible parts, was left out due to the complexity of plant metabolome and the impossibility to properly phenotype it. Recent technical advances in high throughput metabolomic, transcriptomic and genomic platforms have provided efficient approaches to identify new genes and pathways responsible for the extremely diverse plant metabolome. In addition, they allow to establish correlation between genotype and metabolite composition, and to clarify the genetic architecture of complex biochemical pathways, such as the accumulation of secondary metabolites in plants, many of them being highly valuable for the human diet. In this review, we focus on how the combination of metabolomic, transcriptomic and genomic approaches is a useful tool for the selection of crop varieties with improved nutritional value and quality traits.

scholarly journals Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 599
Author(s):  
Miguel A. Gutierrez-Reinoso ◽  
Pedro M. Aponte ◽  
Manuel Garcia-Herreros
Keyword(s):  
Dairy Cattle ◽  
Production Efficiency ◽  
Association Studies ◽  
Phenotypic Traits ◽  
Progeny Testing ◽  
Genome Wide Association Studies ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Increased Risk ◽  
Selection Of

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.

scholarly journals Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 86
Author(s):  
Igor G. Loskutov ◽  
Elena K. Khlestkina
Keyword(s):  
Bioactive Compounds ◽  
Plant Genetic Resources ◽  
Health Benefit ◽  
Cultivated Plants ◽  
Crop Species ◽  
Breeding Programs ◽  
Cereal Grain ◽  
Staple Foods ◽  
Functional Components ◽  
Oat Breeding

Cereal grains provide half of the calories consumed by humans. In addition, they contain important compounds beneficial for health. During the last years, a broad spectrum of new cereal grain-derived products for dietary purposes emerged on the global food market. Special breeding programs aimed at cultivars utilizable for these new products have been launched for both the main sources of staple foods (such as rice, wheat, and maize) and other cereal crops (oat, barley, sorghum, millet, etc.). The breeding paradigm has been switched from traditional grain quality indicators (for example, high breadmaking quality and protein content for common wheat or content of protein, lysine, and starch for barley and oat) to more specialized ones (high content of bioactive compounds, vitamins, dietary fibers, and oils, etc.). To enrich cereal grain with functional components while growing plants in contrast to the post-harvesting improvement of staple foods with natural and synthetic additives, the new breeding programs need a source of genes for the improvement of the content of health benefit components in grain. The current review aims to consider current trends and achievements in wheat, barley, and oat breeding for health-benefiting components. The sources of these valuable genes are plant genetic resources deposited in genebanks: landraces, rare crop species, or even wild relatives of cultivated plants. Traditional plant breeding approaches supplemented with marker-assisted selection and genetic editing, as well as high-throughput chemotyping techniques, are exploited to speed up the breeding for the desired genotуpes. Biochemical and genetic bases for the enrichment of the grain of modern cereal crop cultivars with micronutrients, oils, phenolics, and other compounds are discussed, and certain cases of contributions to special health-improving diets are summarized. Correlations between the content of certain bioactive compounds and the resistance to diseases or tolerance to certain abiotic stressors suggest that breeding programs aimed at raising the levels of health-benefiting components in cereal grain might at the same time match the task of developing cultivars adapted to unfavorable environmental conditions.

scholarly journals High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napusL.)

2016 ◽  
Vol 118 (4) ◽  
pp. 655-665 ◽  
Author(s):  
C. L. Thomas ◽  
N. S. Graham ◽  
R. Hayden ◽  
M. C. Meacham ◽  
K. Neugebauer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Seed Yield ◽  
High Throughput ◽  
Root Traits ◽  
Seedling Root ◽  
High Throughput Phenotyping

scholarly journals Validation of UAV-based alfalfa biomass predictability using photogrammetry with fully automatic plot segmentation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhou Tang ◽  
Atit Parajuli ◽  
Chunpeng James Chen ◽  
Yang Hu ◽  
Samuel Revolinski ◽  
...  
Keyword(s):  
Prediction Model ◽  
High Throughput ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Selection Process ◽  
Forage Legume ◽  
Breeding Programs ◽  
High Throughput Phenotyping ◽  
Fully Automatic ◽  
Uav Images

AbstractAlfalfa is the most widely cultivated forage legume, with approximately 30 million hectares planted worldwide. Genetic improvements in alfalfa have been highly successful in developing cultivars with exceptional winter hardiness and disease resistance traits. However, genetic improvements have been limited for complex economically important traits such as biomass. One of the major bottlenecks is the labor-intensive phenotyping burden for biomass selection. In this study, we employed two alfalfa fields to pave a path to overcome the challenge by using UAV images with fully automatic field plot segmentation for high-throughput phenotyping. The first field was used to develop the prediction model and the second field to validate the predictions. The first and second fields had 808 and 1025 plots, respectively. The first field had three harvests with biomass measured in May, July, and September of 2019. The second had one harvest with biomass measured in September of 2019. These two fields were imaged one day before harvesting with a DJI Phantom 4 pro UAV carrying an additional Sentera multispectral camera. Alfalfa plot images were extracted by GRID software to quantify vegetative area based on the Normalized Difference Vegetation Index. The prediction model developed from the first field explained 50–70% (R Square) of biomass variation in the second field by incorporating four features from UAV images: vegetative area, plant height, Normalized Green–Red Difference Index, and Normalized Difference Red Edge Index. This result suggests that UAV-based, high-throughput phenotyping could be used to improve the efficiency of the biomass selection process in alfalfa breeding programs.

scholarly journals Ryegrass (Lolium perenne) seed yield response to fungicides a summary of 12 years of field research

2009 ◽  
Vol 62 ◽  
pp. 343-348 ◽  
Author(s):  
M.P. Rolston ◽  
B.L. McCloy ◽  
I.C. Harvey ◽  
R.W. Chynoweth
Keyword(s):  
Seed Yield ◽  
Stem Rust ◽  
Field Research ◽  
Reproductive Development ◽  
Yield Response ◽  
Yield Data ◽  
Seed Fill ◽  
Seed Crops ◽  
Seed Yields ◽  
Green Leaf Area

A summary of seed yield data from 19 fungicide trials in perennial and hybrid ryegrass (Lolium spp) seed crops conducted over a 12 year period is presented Seed yields from the best fungicide treatments were increased on average by 25 in forage ryegrass (390 kg/ha) and 42 in turf ryegrass (580 kg/ha) Seed yield increases were associated with the control of stem rust and/or maintaining green leaf area during seed fill In turf ryegrass (susceptible to stem rust) delaying the first fungicide application until stem rust appeared resulted in seed yields that were not different (P>005) from the untreated experimental controls whereas early fungicide applications from the beginning of reproductive development increased seed yield by between 36 and 42 Fungicide mixes of a triazole plus a strobilurin usually gave higher seed yields than using either fungicide type alone

scholarly journals Effects of Mutagens on Morphological traits of Psoralea corylifolia-A Medicinally Important Plant

2020 ◽  
Vol 26 (2) ◽  
Author(s):  
Ajey Karan Chaudhari ◽  
Anand Prakash Singh ◽  
B R Chaudhary
Keyword(s):  
Plant Height ◽  
Seed Yield ◽  
Morphological Traits ◽  
Mutation Breeding ◽  
Yield Potential ◽  
Mutagenic Potential ◽  
Breeding Programs ◽  
Methane Sulphonate ◽  
Flowering Initiation ◽  
Yield Quality

Mutation breeding like in other plants can significantly strengthen medicinal plants breeding programs and help to produce novel varieties with higher yield potential and improved yield quality. The dry and healthy seeds of P. corylifolia IC 111228 were subjected to mutagenic treatments namely ethyl methane sulphonate (EMS) and sodium azide (SA). The treatment concentrations 15mM, 30mM, 45mM and 60mM of EMS and 1mM, 2mM, 3mM and 4mM of SA were chosen to evaluate the mutagenic potential in either case. The morphological traits were evaluated in M1 generation viz. plant height, days to flowering initiation, seed yield/plant and 100-seed weight. In EMS treatment 15 mM increased the plant height and seed yield, while in SA treatment 4 mM increased the seed yield/plant and 100-seed yield.

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