Marker Development in the Genomics Era

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (28 October 2022) | Viewed by 10259

Special Issue Editors


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Guest Editor
Sugarbeet and Potato Research Unit, USDA Agricultural Research Service, Fargo, ND, USA
Interests: plant genetics; chromosome; sugar beet; wheat; maize

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Guest Editor
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
Interests: rice; molecular breeding; data mining

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Guest Editor
College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
Interests: seeds composition; molecular assisted breeding, molecular design; multi-omics resource application; breeding evaluation

Special Issue Information

Dear Colleagues,

Marker-assisted selection (MAS) has played an important role in crop breeding. Single nucleotide polymorphisms (SNPs) are becoming major markers now due to their abundance in genomes and their amenability for high-throughput detection platforms. Significant advances in next-generation sequencing and genomics studies have enabled us to accurately locate SNPs in specific positions in the genome, and association mapping using SNPs covering the whole genome has facilitated the quick identification of markers tightly linked to genes affecting target traits even when an unstructured mapping panel has been used. Several PCR-based SNP detection techniques have been developed in recent years, increasing the flexibility of SNP detection and making SNPs user-friendly markers for either anchoring candidate genes in specific genomic regions or performing efficient selection in breeding. Therefore, to gain insight into marker development in the genomics era, it is our pleasure to organize a Special Issue on “Marker Development in the Genomics Era” to provide an excellent platform and bring together knowledge on using different SNP detection techniques and their applications in gene identification, gene isolation, gene editing, and MAS/genomic selection in breeding to improve host resistance to biotic and abiotic stresses, nutrition, quality, and processing properties.

Dr. Chenggen Chu
Dr. Tianqing Zheng
Dr. Zhaoming Qi
Dr. Xiaojun Nie
Guest Editors

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Keywords

  • marker-assisted selection (MAS)
  • single nucleotide polymorphisms (SNPs)
  • genotype by sequencing (GBS)
  • kompetitive allele specific PCR (KASP)
  • TaqMan
  • rhAmp
  • semi-thermal asymmetric reverse PCR (STARP)
  • candidate gene

Published Papers (4 papers)

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Research

14 pages, 1775 KiB  
Article
Development of the PARMS Markers of the Waxy Gene and Utilization in Discriminating Wild Accessions, and Cultivated Rice (Oryza sativa L.) with Different Eating and Cooking Quality
by Guibeline Charlie Jeazet Dongho Epse Mackon, Enerand Mackon, Yafei Ma, Yitong Zhao, Yuhang Yao, Xianggui Dai and Piqing Liu
Agronomy 2022, 12(6), 1294; https://doi.org/10.3390/agronomy12061294 - 28 May 2022
Cited by 3 | Viewed by 2190
Abstract
Amylose content (AC) is the major indicator of rice eating and cooking quality (ECQ). Its synthesis in rice endosperm is mainly regulated by the protein, granule-bound starch synthase 1, which is encoded by the waxy gene (Os06g0133000, LOC_Os06g04200). The diversity of AC is [...] Read more.
Amylose content (AC) is the major indicator of rice eating and cooking quality (ECQ). Its synthesis in rice endosperm is mainly regulated by the protein, granule-bound starch synthase 1, which is encoded by the waxy gene (Os06g0133000, LOC_Os06g04200). The diversity of AC is largely attributable to the allelic variation at the Wx locus and the development of effective and accurate functional molecular markers to target rice variant alleles is crucial in the breeding strategy. In the present study, we developed six pairs of penta-primer amplification refractory mutation system (PARMS) markers to distinguish between Wxlv, Wxa, Wxin, Wxb, Wxmp, and Wxop,hp. These markers were successfully used to screen the genotype of large assets of genetic resources including 98 wild accessions, 55 cultivars, and 22 parental lines. Our results showed that Wxb in a low AC type was predominant in Guangxi cultivated rice as a result of cultural preference, while Wxlv in the wild accessions. Moreover, our findings surprisingly revealed the presence of Wxb in wild accession, which is a new outcome that may contribute to understanding the origin, selection and domestication processes of rice. These functional markers could be effectively used in marker-assisted breeding to improve selection efficiency of cultivars with desired AC in the early generation. Full article
(This article belongs to the Special Issue Marker Development in the Genomics Era)
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20 pages, 3925 KiB  
Article
Genomic and Transcriptomic Dissection of the Large-Effect Loci Controlling Drought-Responsive Agronomic Traits in Wheat
by Liangjing Cao, Mingjie Lyu, Jingyi Wang, Xuan Wang, Xinchang Li, Ruilian Jing, Jun Liu and Xinwen Hu
Agronomy 2022, 12(6), 1264; https://doi.org/10.3390/agronomy12061264 - 25 May 2022
Viewed by 1941
Abstract
Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the [...] Read more.
Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the genomes of two popular winter wheat cultivars, Lu-Mai 14 and Han-Xuan 10, using a whole-genome re-sequencing assay. There were 4972 loss-of-function mutations carried by protein-coding genes, such as CCA1/LHY, AGO1, ABI3/VP1, EIN3, TPP, and ARFs. We carried out a time-course abscisic acid (ABA)-treatment experiment and profiled 61,251 expressed genes in the roots using a strand-specific RNA sequencing approach. A large number of genes showed time-point specific and/or cultivar-preferential responsive expression patterns. Gene ontology enrichment analysis revealed that ABA-responsive genes were associated with stress-related functions. Among the 20 QTLs, we uncovered 306 expressed genes with high- and/or moderate-effect variations and 472 differentially expressed genes. Detailed analysis and verification of the homozygous genomic variations in the candidate genes encoding sulfotransferase, proteinase, kinase, nitrate transporter, and transcription factors suggested previously unexpected pathways associated with abiotic stress responses in wheat. Full article
(This article belongs to the Special Issue Marker Development in the Genomics Era)
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17 pages, 5293 KiB  
Article
Genetic Dissection of Tobacco (Nicotiana tabacum L.) Plant Height Using Single-Locus and Multi-Locus Genome-Wide Association Studies
by Muhammad Ikram, Ruiqiang Lai, Yanshi Xia, Ronghua Li, Weicai Zhao, Kadambot H. M. Siddique, Jianjun Chen and Peiguo Guo
Agronomy 2022, 12(5), 1047; https://doi.org/10.3390/agronomy12051047 - 27 Apr 2022
Cited by 5 | Viewed by 2115
Abstract
Tobacco (Nicotiana tabacum L.) plant height (PH) is a biologically important plant architecture trait linked to yield and controlled by polygenes. However, limited information is available on quantitative trait nucleotides (QTNs), alleles, and candidate genes. The plant height of 94 tobacco accessions [...] Read more.
Tobacco (Nicotiana tabacum L.) plant height (PH) is a biologically important plant architecture trait linked to yield and controlled by polygenes. However, limited information is available on quantitative trait nucleotides (QTNs), alleles, and candidate genes. The plant height of 94 tobacco accessions and their 126,602 SNPs were measured to conduct a genome-wide association study (GWAS) using four multi-locus (ML) and two single-locus (SL) models to better understand its genetic basis. The ML and SL models detected 181 and 29 QTNs, respectively, across four environments/BLUP; LOD scores ranged from 3.01–13.45, and the phenotypic variance explained (PVE) ranged from 0.69–25.37%. Fifty-two novel, stable QTNs were detected across at least two methods and/or two environments/BLUP, with 0.64–24.76% PVE. Among these, 49 QTNs exhibited significant phenotypic differences between two alleles; the distribution of elite and alternative alleles for each accession ranged from 3–42 and 6–46, respectively, in the mapping population. Seven cross combinations in two directions were predicted using alleles of validated QTNs, including Qinggeng × KY14 for taller plants and RG112 × VA115 for shorter plants. We identified 27 candidate genes in the vicinity of 49 stable QTNs based on comparative genomics, gene ontology (GO), and KEGG enrichment analysis, including AP2, Nitab4.5_0000343g0250.1 (ROC1), Nitab4.5_0000197g0010.1 (VFB1), CDF3, AXR6, KUP8, and NPY2. This is the first study to use genotyping-by-sequencing (GBS) of SNPs to determine QTNs, potential candidate genes, and alleles associated with plant height. These findings could provide a new avenue for investigating the QTNs in tobacco by combining SL and ML association mapping and solid foundations for functional genomics, the genetic basis, and molecular breeding for PH in tobacco. Full article
(This article belongs to the Special Issue Marker Development in the Genomics Era)
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18 pages, 32533 KiB  
Article
Buckwheat Yield Traits Response as Influenced by Row Spacing, Nitrogen, Phosphorus, and Potassium Management
by Ljubiša Kolarić, Vera Popović, Ljubiša Živanović, Nataša Ljubičić, Petar Stevanović, Ljubica Šarčević Todosijević, Divna Simić and Jela Ikanović
Agronomy 2021, 11(12), 2371; https://doi.org/10.3390/agronomy11122371 - 23 Nov 2021
Cited by 19 | Viewed by 2849
Abstract
Buckwheat is an economically important gluten free cereal, and it is a good source of protein, fiber, and energy. The field experiments with buckwheat variety “Novosadska” were set in two experimental years in Pancevo, Serbia. The aim of this study was to determine [...] Read more.
Buckwheat is an economically important gluten free cereal, and it is a good source of protein, fiber, and energy. The field experiments with buckwheat variety “Novosadska” were set in two experimental years in Pancevo, Serbia. The aim of this study was to determine the most optimal technology for buckwheat production. The study aims were to investigate the effects of (1) row spacing: RS1-25 cm and RS2-50 cm; (2) nutrition variants: (N1) 0 kg ha−1 NPK; (N2) NPK 30 kg ha−1; (N3) NPK 60 kg ha−1; and (N4) NPK 90 kg ha−1; (3) environment: Y1-2018 and Y2-2019; and their interactions on the plant height (PH), number of lateral branches (NoLB), mass of seeds per plant (MSP), number of seeds per plant (NoSP), buckwheat grain yield (GY); and (4) the correlations among these traits. All tested parameters of buckwheat significantly varied across row spacing, environment, and nutrition. The average grain yield in the row spacing, RD1-25 cm, was significantly higher than in the wider spacing, RD2-50 cm, and in 2018 than 2019 as well as with the nutrition NPK applied in the amount of 90 kg ha−1 in relation with all the other nutrition variants. All the studied agronomic traits were positively and strongly correlated with GY. Full article
(This article belongs to the Special Issue Marker Development in the Genomics Era)
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