Recent Trends in Oilseed Breeding and Genetics for Agronomical Traits

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 6869

Special Issue Editors

Crop Soil and Environmental Science, Auburn University, Auburn, AL 36830, USA
Interests: peanut; plant breeding; genetics; genomics; GWAS; QTL studies; RNAseq studies
Special Issues, Collections and Topics in MDPI journals
Crop Soil and Environmental Science, Auburn University, Auburn, AL 36830, USA
Interests: plant breeding; genetics; genomics; GWAS; QTL studies; RNAseq studies; epigenetics; cotton; soybean; peanut; grasses
Department of Plant & Microbial Biology, University of California, Berkeley, CA 94704, USA
Interests: genome-wide association mapping; reproductive biology; floral development, genotype-environment (GxE) interactions; seed dormancy; physiology; phytohormones; plant architecture; flowering; sunflowers

Special Issue Information

Dear Colleagues,

High-value edible oilseed crops, such as sunflower, peanut, soybean, sesame, olive, canola, safflower, and palms, provide one of the most valuable commodities in world trade. Studies pursuing to understand oil biosynthesis in plants have ramped up in recent years. Research on oilseed breeding has made substantial progress in altering oil composition, developing better-quality seeds and resistant varieties to insect, pest, and abiotic stress, and improving agronomic traits, thus increasing the overall yield of the crop. Still, it takes much longer to develop a new cultivar through conventional breeding. Recent advances in molecular and genetics tools will be highly effective and speed up the breeding process. The availability of whole-genome sequences of several oilseed crops, cost-effective sequencing techniques, and SNP genotyping arrays have made studies to identify genomic regions and genes conferring better agronomical traits much accessible. In this Special Issue of Plants, we invite research on agronomically essential traits, environmental adaptability, biotic and abiotic stress management, nutritional genomics, studies involving mutant populations, genome-editing, differential gene expression analysis, GWAS studies, mapping of qualitative and quantitative traits, epigenetics, marker-assisted breeding, and strategies to improve oilseed crops.

Prof. Dr. Charles Y. Chen
Dr. Jinesh D Patel
Dr. Srinidhi Holalu
Guest Editors

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Keywords

  • oilseed breeding
  • epigenetics
  • abiotic stress
  • biotic stress
  • differential gene expression
  • genetics
  • genomics
  • genetic diversity
  • marker-assisted breeding
  • bioinformatics
  • seed quality traits
  • seed dormancy

Published Papers (4 papers)

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Research

18 pages, 5019 KiB  
Article
Investigating Variability in Viral Presence and Abundance across Soybean Seed Development Stages Using Transcriptome Analysis
by Hoseong Choi, Yeonhwa Jo, Hyunjung Chung, Soo Yeon Choi, Sang-Min Kim, Jin-Sung Hong, Bong Choon Lee and Won Kyong Cho
Plants 2023, 12(18), 3257; https://doi.org/10.3390/plants12183257 - 13 Sep 2023
Cited by 1 | Viewed by 796
Abstract
Plant transcriptomes offer a valuable resource for studying viral communities (viromes). In this study, we explore how plant transcriptome data can be applied to virome research. We analyzed 40 soybean transcriptomes across different growth stages and identified six viruses: broad bean wilt virus [...] Read more.
Plant transcriptomes offer a valuable resource for studying viral communities (viromes). In this study, we explore how plant transcriptome data can be applied to virome research. We analyzed 40 soybean transcriptomes across different growth stages and identified six viruses: broad bean wilt virus 2 (BBWV2), brassica yellow virus (BrYV), beet western yellow virus (BWYV), cucumber mosaic virus (CMV), milk vetch dwarf virus (MDV), and soybean mosaic virus (SMV). SMV was the predominant virus in both Glycine max (GM) and Glycine soja (GS) cultivars. Our analysis confirmed its abundance in both, while BBWV2 and CMV were more prevalent in GS than GM. The viral proportions varied across developmental stages, peaking in open flowers. Comparing viral abundance measured by viral reads and fragments per kilobase of transcript per million (FPKM) values revealed insights. SMV showed similar FPKM values in GM and GS, but BBWV2 and CMV displayed higher FPKM proportions in GS. Notably, the differences in viral abundance between GM and GS were generally insignificant based on the FPKM values across developmental stages, except for the apical bud stage in four GM cultivars. We also detected MDV, a multi-segmented virus, in two GM samples, with variable proportions of its segments. In conclusion, our study demonstrates the potential of plant transcriptomes for virome research, highlighting their strengths and limitations. Full article
(This article belongs to the Special Issue Recent Trends in Oilseed Breeding and Genetics for Agronomical Traits)
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18 pages, 12508 KiB  
Article
Moderate Salinity Stress Increases the Seedling Biomass in Oilseed Rape (Brassica napus L.)
by Beini Chen, Xiaobo Bian, Mengxin Tu, Tao Yu, Lixi Jiang, Yunhai Lu and Xiaoyang Chen
Plants 2023, 12(8), 1650; https://doi.org/10.3390/plants12081650 - 14 Apr 2023
Cited by 4 | Viewed by 1673
Abstract
Oilseed rape (Brassica napus L.), an important oil crop of the world, suffers various abiotic stresses including salinity stress during the growth stage. While most of the previous studies paid attention to the adverse effects of high salinity stress on plant growth [...] Read more.
Oilseed rape (Brassica napus L.), an important oil crop of the world, suffers various abiotic stresses including salinity stress during the growth stage. While most of the previous studies paid attention to the adverse effects of high salinity stress on plant growth and development, as well as their underlying physiological and molecular mechanisms, less attention was paid to the effects of moderate or low salinity stress. In this study, we first tested the effects of different concentrations of NaCl solution on the seedling growth performance of two oilseed rape varieties (CH336, a semi-winter type, and Bruttor, a spring type) in pot cultures. We found that moderate salt concentrations (25 and 50 mmol L−1 NaCl) can stimulate seedling growth by a significant increase (10~20%, compared to controls) in both above- and underground biomasses, as estimated at the early flowering stage. We then performed RNA-seq analyses of shoot apical meristems (SAMs) from six-leaf-aged seedlings under control (CK), low (LS, 25 mmol L−1), and high (HS, 180 mmol L−1) salinity treatments in the two varieties. The GO and KEGG enrichment analyses of differentially expressed genes (DEGs) demonstrated that such a stimulating effect on seedling growth by low salinity stress may be caused by a more efficient capacity for photosynthesis as compensation, accompanied by a reduced energy loss for the biosynthesis of secondary metabolites and redirecting of energy to biomass formation. Our study provides a new perspective on the cultivation of oilseed rape in saline regions and new insights into the molecular mechanisms of salt tolerance in Brassica crops. The candidate genes identified in this study can serve as targets for molecular breeding selection and genetic engineering toward enhancing salt tolerance in B. napus. Full article
(This article belongs to the Special Issue Recent Trends in Oilseed Breeding and Genetics for Agronomical Traits)
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18 pages, 3067 KiB  
Article
Phosphorus Application Enhances Root Traits, Root Exudation, Phosphorus Use Efficiency, and Seed Yield of Soybean Genotypes
by Mohammad Salim, Yinglong Chen, Zakaria M. Solaiman and Kadambot H. M. Siddique
Plants 2023, 12(5), 1110; https://doi.org/10.3390/plants12051110 - 01 Mar 2023
Cited by 4 | Viewed by 1542
Abstract
Phosphorus (P) is a vital macronutrient required for soybean growth and development but is a finite resource in agriculture worldwide. Low inorganic P availability in soil is often a significant constraint for soybean production. However, little is known about the response of P [...] Read more.
Phosphorus (P) is a vital macronutrient required for soybean growth and development but is a finite resource in agriculture worldwide. Low inorganic P availability in soil is often a significant constraint for soybean production. However, little is known about the response of P supply on agronomic, root morphology, and physiological mechanisms of contrasting soybean genotypes at various growth stages and the possible effects of different P on soybean yield and yield components. Therefore, we conducted two concurrent experiments using the soil-filled pots with six genotypes (deep-root system: PI 647960, PI 398595, PI 561271, PI 654356; and shallow-root system: PI 595362, PI 597387) and two P levels [0 (P0) and 60 (P60) mg P kg−1 dry soil] and deep PVC columns with two genotypes (PI 561271 and PI 595362) and three P levels [0 (P0), 60 (P60), and 120 (P120) mg P kg−1 dry soil] in a temperature-controlled glasshouse. The genotype × P level interaction showed that increased higher P supply increased leaf area, shoot and root dry weights, total root length, shoot, root, and seed P concentrations and contents, P use efficiency (PUE), root exudation, and seed yield at different growth stages in both experiments. At the vegetative stage (Experiment 1), shallow-rooted genotypes with shorter life cycles had more root dry weight (39%) and total root length (38%) than deep-rooted genotypes with longer life cycles under different P levels. Genotype PI 654356 produced significantly higher (22% more) total carboxylates than PI 647960 and PI 597387 under P60 but not at P0. Total carboxylates positively correlated with root dry weight, total root length, shoot and root P contents, and physiological PUE. The deep-rooted genotypes (PI 398595, PI 647960, PI 654356, and PI 561271) had the highest PUE and root P contents. In Experiment 2, at the flowering stage, genotype PI 561271 had the greatest leaf area (202%), shoot dry weight (113%), root dry weight (143%), and root length (83%) relative to the short-duration, shallow-rooted genotype PI 595362 with external P applied (P60 and P120), with similar trends at maturity. PI 595362 had a greater proportion of carboxylates as malonate (248%), malate (58%), and total carboxylates (82%) than PI 561271 under P60 and P120 but no differences at P0. At maturity, the deep-rooted genotype PI 561271 had greater shoot, root, and seed P contents and PUE than the shallow-rooted genotype PI 595362 under increased P rates but no differences at P0. Further, the genotype PI 561271 had higher shoot (53%), root (165%), and seed yield (47%) than PI 595362 with P60 and P120 than P0. Therefore, inorganic P application enhances plant resistance to the soil P pool and maintains high soybean biomass production and seed yield. Full article
(This article belongs to the Special Issue Recent Trends in Oilseed Breeding and Genetics for Agronomical Traits)
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15 pages, 4140 KiB  
Article
Insights into the Genomic Architecture of Seed and Pod Quality Traits in the U.S. Peanut Mini-Core Diversity Panel
by Jinesh D. Patel, Ming Li Wang, Phat Dang, Chris Butts, Marshall Lamb and Charles Y. Chen
Plants 2022, 11(7), 837; https://doi.org/10.3390/plants11070837 - 22 Mar 2022
Cited by 4 | Viewed by 1648
Abstract
Traits such as seed weight, shelling percent, percent sound mature kernels, and seed dormancy determines the quality of peanut seed. Few QTL (quantitative trait loci) studies using biparental mapping populations have identified QTL for seed dormancy and seed grade traits. Here, we report [...] Read more.
Traits such as seed weight, shelling percent, percent sound mature kernels, and seed dormancy determines the quality of peanut seed. Few QTL (quantitative trait loci) studies using biparental mapping populations have identified QTL for seed dormancy and seed grade traits. Here, we report a genome-wide association study (GWAS) to detect marker–trait associations for seed germination, dormancy, and seed grading traits in peanut. A total of 120 accessions from the U.S. peanut mini-core collection were evaluated for seed quality traits and genotyped using Axiom SNP (single nucleotide polymorphism) array for peanut. We observed significant variation in seed quality traits in different accessions and different botanical varieties. Through GWAS, we were able to identify multiple regions associated with sound mature kernels, seed weight, shelling percent, seed germination, and dormancy. Some of the genomic regions that were SNP associated with these traits aligned with previously known QTLs. For instance, QTL for seed dormancy has been reported on chromosome A05, and we also found SNP on the same chromosome associated with seed dormancy, explaining around 20% of phenotypic variation. In addition, we found novel genomic regions associated with seed grading, seed germination, and dormancy traits. SNP markers associated with seed quality and dormancy identified here can accelerate the selection process. Further, exploring the function of candidate genes identified in the vicinity of the associated marker will assist in understanding the complex genetic network that governs seed quality. Full article
(This article belongs to the Special Issue Recent Trends in Oilseed Breeding and Genetics for Agronomical Traits)
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