Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats

Huang, Cheng Tung; Klos, Kathy Esvelt; Huang, Yung‐Fen

doi:10.1534/g3.120.401602

Cited by 8 publications

(6 citation statements)

References 83 publications

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“… Nagel et al , 2012 ). Recently, germination/growth pouches have been utilized to study root traits in plants ( Acharya et al , 2017 ; Huang et al , 2020 ). However, the plant root is a three-dimensional (3D) structure and the results from 2D techniques are often difficult to extrapolate to field conditions ( Topp et al , 2013 ).…”

Section: Can Image-based Methods Be Used To Phenotype For Waterloggin...mentioning

confidence: 99%

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Langan

Bernád

Walsh

et al. 2022

Journal of Experimental Botany

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Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we aim to highlight efforts utilising phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilised to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods and future trends using plant-imaging methods. If effectively utilised to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.

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Section: Can Image-based Methods Be Used To Phenotype For Waterloggin...mentioning

confidence: 99%

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Langan

Bernád

Walsh

et al. 2022

Journal of Experimental Botany

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“…In addition, Huang et al (2020) reported robust approach associated (FarmCPU) with seed vigor traits in two different locations by establishing a new phenotyping pipeline in 650 elite oat breeding lines from CORE (Collaborative Oat Research Enterprise) material. They determined the candidate marker and QTL for the first time by GWAS mapping based on strong statistical method, 2 of 41 SNP genomic regions determined for root traits affecting seed vigor were not mapped, other markers were distributed in 16 linkage groups, 16 associated with stem traits, which are other seed vigor factor, were not mapped.…”

Section: Candidate Gene Association Mapping Analysismentioning

confidence: 99%

Association Mapping of Germination and Some Early Seedling Stage Traits of a Turkish Origin Oat Collection

KOÇAK

Kılınç

Bardak

et al. 2022

Turkish Journal of Field Crops

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In recent years, oat plant especially for hay yield is on demand in Turkey. In this study, 167 oat landraces originated from Turkey were evaluated for germination and some early seedling stage traits and genotyped by 6K SNP Chip assay to detect candidate markers using association mapping analysis. Principal component analysis (PCA) were also performed to determine relationships among investigated traits. The variation in local oat genotypes for germination and other investigated traits was found significant at the 5% significance level, except for germination rate (GR). The values for germination rate was found between 52-76% and 52-100% for germination ratio, while 12.33 to 45 mm for coleoptile length and 8 to 21 mm for radicle length. On the other hand, plumula length varied between 2 to 28.45 mm and 1301.33 to 5494.40 for seed vigor index. In the research, PC1 and PC2 value was found 41.5% and 21.5%, respectively, explaining the 63% of the total variation. Germination rate and germination ratio (GP) were positively and significantly correlated with the other investigated traits. According to the results of the association mapping analysis a total number of 43 candidate markers were observed, 10 candidate markers for germination rate, five candidate markers for germination ratio (GP), five markers for radicle length (RL), eight markers for coleoptile length (CL), seven markers for plumula length (PL) and eight markers for seed vigor index (SVI). These candidate markers identified in this study for germination and early seedling stage traits could be used in future studies.

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“…In maize, RILs have been used to identify seed vigor QTLs associated with seed maturity stage at harvest (Jing-bao et al 2011), seed longevity (Han et al 2018), tolerance of stressful germination conditions (Han et al 2014), and after artificial aging (Wu et al 2020). In barley and oat, QTLs been paired with to identify candidate vigor genes (Thabet et al 2018;Huang et al 2020).…”

Section: Current Approaches To Improve Seed Vigor Seed Priming/treatingmentioning

confidence: 99%

Seed germination and vigor: ensuring crop sustainability in a changing climate

2022

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In the coming decades, maintaining a steady food supply for the increasing world population will require high-yielding crop plants which can be productive under increasingly variable conditions. Maintaining high yields will require the successful and uniform establishment of plants in the field under altered environmental conditions. Seed vigor, a complex agronomic trait that includes seed longevity, germination speed, seedling growth, and early stress tolerance, determines the duration and success of this establishment period. Elevated temperature during early seed development can decrease seed size, number, and fertility, delay germination and reduce seed vigor in crops such as cereals, legumes, and vegetable crops. Heat stress in mature seeds can reduce seed vigor in crops such as lettuce, oat, and chickpea. Warming trends and increasing temperature variability can increase seed dormancy and reduce germination rates, especially in crops that require lower temperatures for germination and seedling establishment. To improve seed germination speed and success, much research has focused on selecting quality seeds for replanting, priming seeds before sowing, and breeding varieties with improved seed performance. Recent strides in understanding the genetic basis of variation in seed vigor have used genomics and transcriptomics to identify candidate genes for improving germination, and several studies have explored the potential impact of climate change on the percentage and timing of germination. In this review, we discuss these recent advances in the genetic underpinnings of seed performance as well as how climate change is expected to affect vigor in current varieties of staple, vegetable, and other crops.

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Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats

Cited by 8 publications

References 83 publications

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Association Mapping of Germination and Some Early Seedling Stage Traits of a Turkish Origin Oat Collection

Seed germination and vigor: ensuring crop sustainability in a changing climate

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