Molecular Quantitative Genetics Applied to Plant Breeding

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 9378

Special Issue Editors

Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: agronomy; crop breeding; intra-species competition; low-input agriculture; preservation and utilization of plant genetic resources
Institute of Applied Biosciences, The Centre for Research and Technology, Hellas, 57001 Thessaloníki, Greece
Interests: genomics; plant breeding; CRISP/R; stress tolerance; molecular genetics; population genetics molecular species identification and authentication
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Special Issue Information

Dear Colleagues,

Quantitative genetics has been used by plant breeders over the years to systematically select germplasm for crop improvement. This has been enhanced with the use of molecular markers, which enabled the identification of genes or quantitative trait loci (QTL), and consequently marker-assisted selection, for economically-important traits of interest. Advances in molecular marker and computer technologies have contributed to significant progress in the field of plant molecular quantitative genetics. The development of single-nucleotide polymorphism markers enables high-throughput genotyping at a lower cost. Modern computers can analyze large datasets, as well as conduct simulations, using complex statistical models. These recent developments are expected to improve efficiency in selecting the germplasm whose genotypic values best meet the breeder’s objectives.

The scope of this Special Issue covers different applications of molecular quantitative genetics in crop improvement, which includes, but is not limited to, QTL mapping, genome-wide association studies (GWAS), marker-assisted selection, and genomic selection. All types of articles, such as original research, opinions, and reviews, are welcome.

Prof. Dr. Ioannis Tokatlidis
Dr. Panagiotis Madesis
Guest Editors

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Keywords

  • Plant breeding
  • Molecular genetics
  • Quantitative genetics
  • Population genetics
  • Genomics
  • Statistics
  • Marker-assisted selection
  • QTL mapping
  • Genome-wide association studies (GWAS)
  • Genomic prediction

Published Papers (3 papers)

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Research

16 pages, 1351 KiB  
Article
The Quantitative Genetics of Flowering Traits in Wide Crosses of Chickpea
by Abdulkarim Lakmes, Abdullah Jhar, R. Varma Penmetsa, Wenbin Wei, Adrian C. Brennan and Abdullah Kahriman
Agriculture 2022, 12(4), 486; https://doi.org/10.3390/agriculture12040486 - 30 Mar 2022
Cited by 6 | Viewed by 3364
Abstract
Chickpea (Cicer arietinum L.) is one of the most ımportant food legume crops in the world. Chickpea is valued for its nutritive seed composition, which is high in protein content and used increasingly as a substitute for animal protein. Days to fırst [...] Read more.
Chickpea (Cicer arietinum L.) is one of the most ımportant food legume crops in the world. Chickpea is valued for its nutritive seed composition, which is high in protein content and used increasingly as a substitute for animal protein. Days to fırst flowerıng is an important component of the adaptation and productivity of chickpea in rainfed environments characterized by terminal drought and heat stress. This study aimed to identify the inheritance pattern and identify quantitative trait loci (QTLs) for days to first flowering and flowering color in F2:4 generation nested association mapping (NAM) populations of chickpea obtained using wide crosses between Gokce as the cultivated variety and wild accessions of C. reticulatum and C. echinospermum. A total of ten populations of 113 to 191 individuals each were grown under field conditions near Sanliurfa, Turkey. Two populations were genotyped for 46 single nucleotide polymorphism (SNP) markers, enabling QTL analysis. Flowering time differed between families, with the frequency distributions indicating quantitative inheritance controlled by both genes of major and minor effects. Three significant QTLs for the flowering time were mapped in one mapping family. For flower color, chi-square tests showed that five populations accepted single-gene action, two populations accepted two-gene action, and three populations accepted neither model. Two significant QTLs at three genomic regions were identified across the two genotyped populations. Days to first flowering was positively correlated with flower color for two of the ten populations. The diversity of QTLs identified underscored the potential of crop wild relatives of chickpea as sources of novel alleles for chickpea breeding. Full article
(This article belongs to the Special Issue Molecular Quantitative Genetics Applied to Plant Breeding)
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14 pages, 19172 KiB  
Article
QTL Mapping of Somatic Regeneration-Related Traits in Maize
by Liqiang Dai, Yan Zhang, Siping Han and Dongyun Hao
Agriculture 2022, 12(3), 393; https://doi.org/10.3390/agriculture12030393 - 11 Mar 2022
Cited by 2 | Viewed by 1880
Abstract
The somatic regeneration of maize depends on its genotypes, so improving its variety with modern biotechnology is severely restricted. Locating the quantitative trait loci (QTLs) associated with somatic regeneration is important for breeding elite inbred lines that undergo genetic transformations. Here, by crossing [...] Read more.
The somatic regeneration of maize depends on its genotypes, so improving its variety with modern biotechnology is severely restricted. Locating the quantitative trait loci (QTLs) associated with somatic regeneration is important for breeding elite inbred lines that undergo genetic transformations. Here, by crossing the high-regeneration inbred line H99 and non-regeneration inbred line Fr993, an F2 population and its F2:3 and F2:4 population families were constructed. Immature embryos from the family populations were subjected to tissue culture in two independent seasons to determine their embryogenic callus induction rates (EIRs), green callus rates (GCRs) and plantlet regeneration rates (PRRs). Genetic linkage maps were constructed for the F2 population to locate somatic regeneration QTLs. The results showed that variation in the EIR, GCR and PRR ranged from 0.00–99.33%, and their broad-sense heritabilities were 0.50, 0.52 and 0.53, respectively. The total genetic distance of the linkage maps constructed by the GenoBaits 10 K chip was 2319.50 cM, and twelve QTLs were associated with somatic regeneration traits, accounting for 3.90–14.06% of the phenotypic variation. Expression analysis revealed six candidate genes screened from the QTLs with distinct responses to induction culture in the parental lines, suggesting that they may impact commitment to somatic cell fate. These results provide a basis for the molecular breeding of maize varieties with high-frequency somatic regeneration. Full article
(This article belongs to the Special Issue Molecular Quantitative Genetics Applied to Plant Breeding)
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15 pages, 2307 KiB  
Article
InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.)
by Huanran Yuan, Weilong Yang, Jianing Zou, Mingxing Cheng, Fengfeng Fan, Ting Liang, Yajie Yu, Ronghua Qiu, Shaoqing Li and Jun Hu
Agriculture 2021, 11(7), 655; https://doi.org/10.3390/agriculture11070655 - 11 Jul 2021
Cited by 4 | Viewed by 2771
Abstract
A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms in gene mapping, analysing genetic diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, a re-sequencing project, discovered millions of genome-wide InDels. We found that the [...] Read more.
A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms in gene mapping, analysing genetic diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, a re-sequencing project, discovered millions of genome-wide InDels. We found that the proportion of >50-bp long InDels (699,475) of the total (1,248,503) is 56.02%. The number of InDels on each chromosome was consistent with the corresponding chromosome length. The maximum InDels were on chromosome 1 (78,935), and the minimum InDels were on chromosome 9 (41,752), with an average density of 1.87 InDels/kb (range: 1.50–2.36 InDels/kb). Furthermore, 96 InDels of about 3.98 Mb/InDel were selected to detect the polymorphism. The results exhibited ideal performance in 2% agarose gel electrophoresis. Phylogenetic analysis exhibited that InDel markers had excellent polymorphisms between rice varieties of japonica and indica, and varieties could be classified based on the statistical results of their polymorphisms. The InDel markers could be applied to identify the recombinant inbred lines in a population. These results reveal that the high-density long InDel markers could help us examine the functional diversity, species variation, and map-based cloning. Full article
(This article belongs to the Special Issue Molecular Quantitative Genetics Applied to Plant Breeding)
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