QTL Mapping of Seed Quality Traits in Crops, 2nd Edition

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 1256

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Guest Editor
Plant Genomics and Biotechnology Lab, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
Interests: plant genetics, genomics, and biotechnology; QTL mapping of important agronomic traits especially seed composition traits in soybean and other crops
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Dear Colleagues,

Seeds of major crops are rich in valuable compounds that are essential for the food and feed industries. The nutritional and health benefits of animal feed and human diets rely heavily on seed-derived proteins, amino acids, oils, fatty acids (such as palmitic, stearic, oleic, linoleic, linolenic acids), sugars (including glucose, galactose, sucrose, raffinose), isoflavones (daidzein, genistein, glycitein), vitamins, minerals, secondary metabolites, and other nutrients. Understanding the genetic basis of these beneficial compounds is critical. Over the past three decades, numerous studies have been conducted to identify and map the quantitative trait loci (QTL) associated with these traits. However, many of these QTL regions remain poorly characterized, with most candidate genes still unidentified.

This Special Issue of Plants aims to advance the field by focusing on the genetic and QTL mapping of seed quality traits in crops, utilizing both traditional mapping populations (such as recombinant inbred lines (RILs), F2, doubled haploid, etc.) and genome-wide association studies (GWAS). Submissions that identify candidate genes within the identified QTL regions are especially encouraged.

We also welcome papers that integrate artificial intelligence (AI) and machine learning (ML) techniques in the analysis of genetic and QTL data. AI and ML offer powerful tools for uncovering hidden patterns, predicting trait outcomes, and enhancing the precision of QTL mapping and candidate gene identification. Studies leveraging these advanced computational approaches to gain new insights into seed quality traits are highly welcomed. We look forward to receiving your valuable contributions to this Special Issue.

Prof. Dr. Abdelmajid Kassem
Guest Editor

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Keywords

  • crops
  • QTL mapping
  • seed quality traits
  • GWAS
  • seed protein
  • oil
  • fatty acids
  • amino acids
  • sugars
  • isoflavones
  • AI
  • ML

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Published Papers (2 papers)

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Research

13 pages, 2575 KiB  
Article
Mapping of a Quantitative Trait Locus for Stay-Green Trait in Common Wheat
by Xin Li, Xin Bai, Lijuan Wu, Congya Wang, Xinghui Liu, Qiqi Li, Xiaojun Zhang, Fang Chen, Chengda Lu, Wei Gao and Tianling Cheng
Plants 2025, 14(5), 727; https://doi.org/10.3390/plants14050727 - 27 Feb 2025
Viewed by 482
Abstract
The stay-green (SG) trait enhances photosynthetic activity during the late grain-filling period, benefiting grain yield under drought and heat stresses. CH7034 is a wheat breeding line with SG. To clarify the SG loci carried by CH7034 and obtain linked molecular markers, in this [...] Read more.
The stay-green (SG) trait enhances photosynthetic activity during the late grain-filling period, benefiting grain yield under drought and heat stresses. CH7034 is a wheat breeding line with SG. To clarify the SG loci carried by CH7034 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross between CH7034 and non-SG SY95-71 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2159 SNP markers was constructed. Then, the chlorophyll content of flag leaf from each RIL was estimated for mapping, and one QTL for SG on chromosome 7D was identified, temporarily named QSg.sxau-7D, with the maximum phenotypic variance explained of 8.81~11.46%. A PCR-based diagnostic marker 7D-16 for QSg.sxau-7D was developed, and the CH7034 allele of 7D-16 corresponded to the higher flag leaf chlorophyll content, while the 7D-16 SY95-71 allele corresponded to the lower value, which confirmed the genetic effect on SG of QSg.sxau-7D. QSg.sxau-7D located in the 526.4~556.2 Mbp interval is different from all the known SG loci on chromosome 7D, and 69 high-confidence annotated genes within the interval expressed throughout the entire period of flag leaf senescence. Moreover, results of an association analysis based on the diagnostic marker showed that there is a positive correlation between QSg.sxau-7D and thousand-grain weight. Our results revealed a novel QTL QSg.sxau-7D whose CH7034 allele had a strong effect on SG, which can be applied in further wheat molecular breeding. Full article
(This article belongs to the Special Issue QTL Mapping of Seed Quality Traits in Crops, 2nd Edition)
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15 pages, 2927 KiB  
Article
Identification of a New Major Oil Content QTL Overlapped with FAD2B in Cultivated Peanut (Arachis hypogaea L.)
by Feifei Wang, Huarong Miao, Shengzhong Zhang, Xiaohui Hu, Chunjuan Li, Weiqiang Yang and Jing Chen
Plants 2025, 14(4), 615; https://doi.org/10.3390/plants14040615 - 18 Feb 2025
Viewed by 452
Abstract
High oil content in peanut seeds is a key breeding objective for peanut (Arachis hypogaea L.) quality improvement. In order to explore the genetic basis of oil content in peanuts, a recombinant inbred line (RIL) population consisting of 256 lines was phenotyped [...] Read more.
High oil content in peanut seeds is a key breeding objective for peanut (Arachis hypogaea L.) quality improvement. In order to explore the genetic basis of oil content in peanuts, a recombinant inbred line (RIL) population consisting of 256 lines was phenotyped across six environments. Continuous distribution and transgressive segregation for both oil content and oleic acid content were demonstrated across all environments. Quantitative trait locus (QTL) analysis yielded 15 additive QTLs explaining 4.34 to 23.10% of phenotypic variations. A novel stable and major QTL region conditioning oil content (qOCB09.1) was mapped to chromosome B09, spanning a 1.99 Mb genomic region with 153 putative genes, including the oleic acid gene FAD2B, which may influence the oil content. Candidate genes were identified and diagnostic markers for this region were developed for further investigation. Additionally, 18 pairs of epistatic interactions involving 35 loci were identified to affect the oil content, explaining 1.25 to 1.84% of phenotypic variations. These findings provide valuable insights for further map-based cloning of favorable alleles for oil content in peanuts. Full article
(This article belongs to the Special Issue QTL Mapping of Seed Quality Traits in Crops, 2nd Edition)
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