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Agriculture
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Trait Genetics and Molecular Mapping of Genes in Food and...
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Trait Genetics and Molecular Mapping of Genes in Food and Forage Crops

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 7706

Special Issue Editors

Dr. Prabin Bajgain

E-Mail Website
Guest Editor
Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, USA
Interests: perennial crop breeding and genetics; crop genomics; crop domestication; computational biology; genomic prediction
Dr. Steve Larson

E-Mail Website
Guest Editor
USDA ARS, Forage and Range Research, UMC 6300, Logan, UT 84322, USA
Interests: forages; quantitative trait loci; genotyping; genetic diversity; genetic mapping
Dr. Xiaofei Zhang

E-Mail
Guest Editor
Alliance of Bioversity International and CIAT, Rome, Italy
Interests: plant breeding; trait discovery and deployment; genomics-assisted breeding; genetic gain

Special Issue Information

Dear Colleagues,

The development of advanced crop and forage germplasm usually relies on improving important agronomic and quality traits to meet the needs of farmers, consumers and processors. Trait improvement in plant breeding populations is achieved using phenotypic selection or genetic (marker-assisted or genome-wide) selection, and oftentimes both. The efficiency of these selection steps depends on the genetic characterization of important traits and identification of genomic loci controlling the traits. In other words, efforts in trait genetics and molecular mapping of genes in food and forage crops to help uncover genomic regions and associated molecular markers are vital in developing advanced germplasm. As next-generation sequencing and other high-throughput genotyping platforms continue to be cheaper every year, crop breeding has benefitted from the application of these technologies in the discovery of genomic regions associated with traits of interest. Mapping of QTLs and diagnostic marker discovery have led to a better understanding of trait expression in all crop types, thereby aiding in the development of better varieties. It is only imperative that we continue to recognize and highlight such efforts so that plant breeders and geneticists around the world can benefit from this collective knowledge.

The aim of this issue is to expand our current understanding of trait genetics and genetic mapping of important traits in crop breeding. It seeks to highlight research work conducted in mainstream and novel settings. Both original research articles and review articles are welcome.

Dr. Prabin Bajgain
Dr. Steve Larson
Dr. Xiaofei Zhang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • crop breeding
  • trait discovery
  • trait improvement
  • QTL mapping
  • gene discovery
  • marker-assisted selection
  • genetic gain

Published Papers (2 papers)

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Research

15 pages, 2123 KiB  
Article
Identifying New Resistance to Cassava Mosaic Disease and Validating Markers for the CMD2 Locus
by Cu Thi Le Thuy, Luis Augusto Becerra Lopez-Lavalle, Nguyen Anh Vu, Nguyen Huu Hy, Pham Thi Nhan, Hernan Ceballos, Jonathan Newby, Nguyen Ba Tung, Nguyen Trong Hien, Le Ngoc Tuan, Nguyen Hung, Nguyen Thi Hanh, Do Thi Trang, Pham Thi Thu Ha, Le Huy Ham, Xuan Hoi Pham, Do Thi Nhu Quynh, Ismail Y. Rabbi, Peter A. Kulakow and Xiaofei Zhang
Agriculture 2021, 11(9), 829; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture11090829 - 30 Aug 2021
Cited by 7 | Viewed by 3823
Abstract
Cassava (Manihot esculenta Crantz) is a crucial staple crop, and provides carbohydrate energy to more than half a billion people in the tropics. Cassava mosaic disease (CMD) is the most important disease of cassava in Africa. Since Sri Lanka Cassava Mosaic Virus [...] Read more.
Cassava (Manihot esculenta Crantz) is a crucial staple crop, and provides carbohydrate energy to more than half a billion people in the tropics. Cassava mosaic disease (CMD) is the most important disease of cassava in Africa. Since Sri Lanka Cassava Mosaic Virus (SLCMV) was first reported in South East Asia in 2015, establishing sustainable solutions to CMD has become a top priority for the cassava program at the International Center for Tropical Agriculture (CIAT) and its partners. In the present study, we screened two populations for CMD resistance: VNM142, 142 clones collected from farms throughout Vietnam, and CIAT102, 102 clones resistant to CMD or mites, which were introduced from CIAT. High broad-sense heritability was observed in all the trials (>0.80). From the population VNM142, eight clones showed high CMD resistance with CMD severity scores less than 2.0. Two resistant clones had the same DNA fingerprinting with the accessions CR63 (PER262 or TAI9) and KM57 (VNM8) in the genebank, respectively. To our knowledge, this is the first report of CMD resistance in the genebank at CIAT. We also used the two populations to validate the CMD markers S12_7926132 and S14_4626854. Both markers explained 51% of the population variance in the segregating population CIAT102, but only 11% in the diverse population VNM142. Thus, we concluded that the two CMD markers could not be used to select for CMD resistance in diverse populations, but could predict the CMD resistance in segregating populations when the susceptible parents do not have resistant marker alleles and the resistance of the CMD2 donors is confirmed. Full article
(This article belongs to the Special Issue Trait Genetics and Molecular Mapping of Genes in Food and Forage Crops)
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15 pages, 2079 KiB  
Article
Multi-Allelic Haplotype-Based Association Analysis Identifies Genomic Regions Controlling Domestication Traits in Intermediate Wheatgrass
by Prabin Bajgain and James A. Anderson
Agriculture 2021, 11(7), 667; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture11070667 - 15 Jul 2021
Cited by 8 | Viewed by 2859
Abstract
Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscapes. This study genetically maps six domestication [...] Read more.
Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscapes. This study genetically maps six domestication traits in the fourth cycle IWG breeding population at the University of Minnesota: height, seed length, seed width, shattering, threshability, and seed mass. A weak population structure was observed and linkage disequilibrium (r2) declined rapidly: 0.23 mega base pairs at conventional r2 value of 0.2. Broad-sense heritabilities were overall high and ranged from 0.71–0.92. Association analysis was carried out using 25,909 single SNP markers and 5379 haplotype blocks. Thirty-one SNP markers and 17 haplotype blocks were significantly associated with the domestication traits. These associations were of moderate effect as they explained 4–6% of the observed phenotypic variation. Ten SNP markers were also detected by the haplotype association analysis. One SNP marker on Chromosome 8, also discovered in haplotype block analysis, was common between seed length and seed mass. Increasing the frequency of favorable alleles in IWG populations via marker-assisted selection and genomic selection is an effective approach to improve IWG’s domestication traits. Full article
(This article belongs to the Special Issue Trait Genetics and Molecular Mapping of Genes in Food and Forage Crops)
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