Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

Frontiers in Genetics, Год журнала: 2021, Номер 12

Опубликована: Фев. 24, 2021

Although hybrid crop varieties are among the most popular agricultural innovations, rationale for breeding is sometimes misunderstood. Hybrid slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection exploitation heterosis simultaneously. Inbred parental lines can identically reproduce both themselves their F

Язык: Английский

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Genetic and Phenotypic Evaluation of European Maize Landraces as a Tool for Conservation and Valorization of Agrobiodiversity

Biology, Год журнала: 2024, Номер 13(6), С. 454 - 454

Опубликована: Июнь 19, 2024

The ECPGR European Evaluation Network (EVA) for Maize involves genebanks, research institutions, and private breeding companies from nine countries focusing on the valorization of maize genetic resources across Europe. This study describes a diverse collection 626 local landraces traditional varieties (Zea mays L.) including criteria selection its phenotypic diversity. High-throughput pool genotyping grouped into groups with threshold 0.6 admixture, while 277 accessions were designated admixed likely to have resulted previous activities. grouping correlated well geographic origins collection, also reflecting various pathways introduction Phenotypic evaluations 588 flowering time plant architecture in multilocation trials over three years confirmed great diversity within although clusters only partially grouping. EVA approach promotes conservation opens an opportunity increase variability developing improved populations farmers, better adaptation specific environments greater tolerance stresses. As such, provides valuable sources facing climate change due varieties’ adaptation.

Язык: Английский

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Improving Imputation Quality in BEAGLE for Crop and Livestock Data

G3 Genes Genomes Genetics, Год журнала: 2019, Номер 10(1), С. 177 - 188

Опубликована: Ноя. 2, 2019

Imputation is one of the key steps in preprocessing and quality control protocol any genetic study. Most imputation algorithms were originally developed for use human genetics thus are optimized a high level diversity. Different versions BEAGLE evaluated on datasets doubled haploids two European maize landraces, commercial breeding line diversity panel chicken, respectively, with different levels structure which can be taken into account by parameter tuning. Especially phasing 5.0 outperformed newest version (5.1) turn also lead to improved imputation. Earlier far more dependent adaption parameters all our tests. For versions, ne (effective population size) had major effect error rate ungenotyped markers, reducing rates up 98.5%. Further improvement was obtained tuning affecting haplotype cluster that used initialize underlying Hidden Markov Model BEAGLE. The number markers extremely than halved flint reference genome (F7, PE0075 etc.) instead commonly B73. On average, reduced 8.5% excluding genetically distant individuals from chicken panel. To optimize accuracy has find balance between representing as much possible while avoiding introduction noise including individuals.

Язык: Английский

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Discovery of beneficial haplotypes for complex traits in maize landraces

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Окт. 2, 2020

Abstract Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources diversity, but quantitative traits efficient strategies their targeted utilization lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make native diversity early development accessible elite germplasm A comparative genomic analysis the discovered haplotypes landrace-derived and a panel 65 breeding lines, both genotyped with 600k SNPs, points untapped beneficial target landraces. The superior phenotypic performance carrying favorable landrace as compared alternative confirms these findings. Stability haplotype effects across populations environments well limited on undesired indicate that our strategy has potential harnessing genetic resources.

Язык: Английский

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Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions

Journal of Experimental Botany, Год журнала: 2021, Номер 72(17), С. 5942 - 5960

Опубликована: Июль 9, 2021

Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area strongly biased towards species with C3 photosynthesis relative C4 species. Here, we outline potential strategies for yields crops by reviewing the major bottlenecks limiting NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state non-stressed conditions can be enhanced increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative performance drought, heat, chilling stress during induction await further verification. Based on source-sink interactions maize, sugarcane, sorghum, alleviating these establishment growth harvestable parts are likely improve yield. The expected benefits shown augmented trend planting density, increases impact source limitation yields.

Язык: Английский

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High-dimensional sparse vine copula regression with application to genomic prediction

Biometrics, Год журнала: 2024, Номер 80(1)

Опубликована: Янв. 1, 2024

High-dimensional data sets are often available in genome-enabled predictions. Such include nonlinear relationships with complex dependence structures. For such situations, vine copula-based (quantile) regression is an important tool. However, the current approaches do not scale up to high and ultra-high dimensions. To perform high-dimensional sparse regression, we propose 2 methods. First, show their superiority regarding computational complexity over existing Second, define relevant, irrelevant, redundant explanatory variables for quantile regression. Then, our method's power selecting relevant prediction accuracy via simulation studies. Next, apply proposed methods real data, aiming at genomic of maize traits. Some processing feature extraction steps further discussed. Finally, advantage linear models forests studies applications.

Язык: Английский

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Using Local Convolutional Neural Networks for Genomic Prediction

Frontiers in Genetics, Год журнала: 2020, Номер 11

Опубликована: Ноя. 12, 2020

The prediction of breeding values and phenotypes is central importance for both livestock crop breeding. In this study, we analyze the use artificial neural networks (ANN) and, in particular, local convolutional (LCNN) genomic prediction, as a region-specific filter corresponds much better with our prior genetic knowledge on architecture traits than traditional networks. Model performances are evaluated simulated maize data panel (n = 10,000; p 34,595) real Arabidopsis 2,039; 180,000) variety based their predictive ability. baseline LCNN, containing one layer (kernel size: 10) two fully connected layers 64 nodes each, outperforming commonly proposed ANNs (multi perceptrons networks) basically all considered traits. For high heritability large training population present data, LCNN even state-of-the-art methods like best linear unbiased (GBLUP), Bayesian models extended GBLUP, indicated by an increase ability up to 24%. However, small populations, these outperform ANNs. Nevertheless, still outperforms other around 10%. Minor improvements tested network were obtained increasing kernel size reducing stride, whereas number subsequent node sizes had neglectable impact. Although gains scale sets using LCNNs, practical comes additional problems, such need genotyping individuals, lack estimation reliability. Furthermore, additive design, ANN-based estimates not. also new opportunities, can easily be account inputs (omics, weather etc.) outputs (multi-trait models), computing time increases linearly individuals. With advances high-throughput phenotyping cheaper genotyping, become valid alternative prediction.

Язык: Английский

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Remote Sensing of Maize Plant Height at Different Growth Stages Using UAV-Based Digital Surface Models (DSM)

Agronomy, Год журнала: 2022, Номер 12(4), С. 958 - 958

Опубликована: Апрель 15, 2022

Plant height of maize is related to lodging resistance and yield highly heritable but also polygenic, thus an important trait in breeding. Various manual methods exist determine the plant maize, yet they are labor-intensive time consuming. Therefore, we established digital surface models (DSM) based on RGB-images captured by unmanned aerial vehicle (UAV) at five different dates throughout growth period rapidly estimate 400 genotypes. The UAV-based estimation (PHUAV) was compared measurement from ground highest leaf (PHL), tip manually straightened (PHS) and, final date, top tassel (PHT). best results were obtained for estimating both PHL (0.44 ≤ R2 0.51) PHS (0.50 0.61) 39 68 days after sowing (DAS). After calibration mean absolute percentage error (MAPE) between PHUAV a range 12.07% 19.62%. It recommended apply 0.2 m average maturity before plants start senesce change color.

Язык: Английский

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Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next‐generation varieties

Plant Biotechnology Journal, Год журнала: 2023, Номер 21(6), С. 1123 - 1139

Опубликована: Фев. 6, 2023

Landraces, that is, traditional varieties, have a large diversity is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions enlarge the genetic of varieties. As proof concept, pools from 156 American European maize representing 2340 individuals were genotyped with an SNP array assess their genome-wide diversity. They compared elite cultivars produced across 20th century, represented by 327 inbred lines. Detection selective footprints between different geographic origin identified genes involved environmental adaptation (flowering times, growth) tolerance abiotic biotic stress (drought, cold, salinity). Promising developing two indicators estimate contribution genome lines: (i) modified Roger's distance standardized gene (ii) assignation lines using supervised analysis. It showed most do not closely related only 10 landraces, including famous as Reid's Yellow Dent, Lancaster Surecrop Lacaune, cumulated half total Comparison ancestral directly derived more advanced breeding cycles decrease number contribution. New limited contributions enriched haplotype reference than those high Our approach opens avenue for identification pre-breeding.

Язык: Английский

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Can we improve the chilling tolerance of maize photosynthesis through breeding?

Journal of Experimental Botany, Год журнала: 2022, Номер 73(10), С. 3138 - 3156

Опубликована: Фев. 2, 2022

Abstract Chilling tolerance is necessary for crops to thrive in temperate regions where cold snaps and lower baseline temperatures place limits on life processes; this particularly true of tropical origin such as maize. Photosynthesis often adversely affected by chilling stress, yet the maintenance photosynthesis essential healthy growth development, most crucially yield. In review, we describe physiological basis enhancing maize examining nine key responses stress. We synthesize current knowledge genetic variation photosynthetic with respect each these traits summarize extent which mapping candidate genes have been used understand genomic underpinning tolerance. Finally, provide perspectives future breeding advocate holistic high-throughput approaches screen research programmes order develop resilient future.

Язык: Английский

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