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Research on Tropical Food Crop Genomics
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Research on Tropical Food Crop Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 18574

Special Issue Editors

Dr. Michael Abberton

E-Mail Website
Guest Editor
International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
Interests: yam; tropical crop plants; plant genetics and diversity
Dr. Rajneesh Paliwal

E-Mail Website
Guest Editor
The International Institute of Tropical Agriculture, Ibadan, Nigeria
Interests: tropical crops; plant genetics and breeding; climate change

Special Issue Information

Dear Colleagues,

In tropics, crop yield efficiency is determined by a combination of climate factors and, consequently, crop yields are less in the tropics than temperate. Presently, the increasing global warming trend is making crops more vulnerable by dramatically affecting their productivity and the future food security of the tropical regions. Tropical agriculture in Sub-Saharan Africa (SSA) is thought to be the most vulnerable to this climate change, and crop yield could decrease by 6–24% depending on the climate scenario and management strategy.

Crop improvements have played an important role in enhancing crop yields in the past. Crops are currently well-integrated with the cutting-edge technology of both phenomics and genomics, which can mitigate the adverse effect of climate change and contribute to sustainable agriculture and food security of tropical regions, including SSA. Now, crop improvement methods have shifted from conventional plant breeding to molecular plant breeding, which applies several new biotechnology tools integrated with traditional breeding to accelerate genetic gain in a short time for a trait of interest to develop improved cultivars.

Currently, advanced genomic researchers are engaged in tropical crop research to explore germplasm diversity and QTL analysis for different traits, such as flowering, yield-relative traits, insect/pest resistance traits, and disease traits, abiotic stress tolerance traits, and quality.

This Special Issue will be centered on the use of next-generation sequencing for tropical food crop genetics and genomics research to better understand genetic diversity and population structure, linkage mapping, QTL discovery, genome-wide association study (GWAS), marker-assisted selection, and genomic selection.

Dr. Michael Abberton
Dr. Rajneesh Paliwal
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. Genes 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

  • Tropical crops
  • Germplasm
  • Genetics
  • Genomics
  • Genetic diversity
  • Linkage mapping
  • QTL
  • GWAS
  • Marker-assisted selection
  • Genomic selection

Published Papers (6 papers)

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Research

19 pages, 4054 KiB  
Article
Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms)
by Oluwaseyi E. Olomitutu, Rajneesh Paliwal, Ayodeji Abe, Olubusayo O. Oluwole, Olaniyi A. Oyatomi and Michael T. Abberton
Genes 2022, 13(12), 2350; https://doi.org/10.3390/genes13122350 - 13 Dec 2022
Cited by 1 | Viewed by 1862
Abstract
Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately [...] Read more.
Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5–10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB. Full article
(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)
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28 pages, 5329 KiB  
Article
Identification of Genomic Regions Associated with Agronomic and Disease Resistance Traits in a Large Set of Multiple DH Populations
by Kassahun Sadessa, Yoseph Beyene, Beatrice E. Ifie, L. M. Suresh, Michael S. Olsen, Veronica Ogugo, Dagne Wegary, Pangirayi Tongoona, Eric Danquah, Samuel Kwame Offei, Boddupalli M. Prasanna and Manje Gowda
Genes 2022, 13(2), 351; https://doi.org/10.3390/genes13020351 - 15 Feb 2022
Cited by 4 | Viewed by 2867
Abstract
Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African [...] Read more.
Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African region. In this study, 879 doubled haploid (DH) lines derived from 26 biparental populations were evaluated under artificial inoculation of MLN, as well as under well-watered (WW) and water-stressed (WS) conditions for grain yield and other agronomic traits. All DH lines were used for analyses of genotypic variability, association studies, and genomic predictions for the grain yield and other yield-related traits. Genome-wide association study (GWAS) using a mixed linear FarmCPU model identified SNPs associated with the studied traits i.e., about seven and eight SNPs for the grain yield; 16 and 12 for anthesis date; seven and eight for anthesis silking interval; 14 and 5 for both ear and plant height; and 15 and 5 for moisture under both WW and WS environments, respectively. Similarly, about 13 and 11 SNPs associated with gray leaf spot and turcicum leaf blight were identified. Eleven SNPs associated with senescence under WS management that had depicted drought-stress-tolerant QTLs were identified. Under MLN artificial inoculation, a total of 12 and 10 SNPs associated with MLN disease severity and AUDPC traits, respectively, were identified. Genomic prediction under WW, WS, and MLN disease artificial inoculation revealed moderate-to-high prediction accuracy. The findings of this study provide useful information on understanding the genetic basis for the MLN resistance, grain yield, and other agronomic traits under MLN artificial inoculation, WW, and WS conditions. Therefore, the obtained information can be used for further validation and developing functional molecular markers for marker-assisted selection and for implementing genomic prediction to develop superior elite lines. Full article
(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)
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20 pages, 1782 KiB  
Article
Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm
by Alimatu Sadia Osuman, Baffour Badu-Apraku, Benjamin Karikari, Beatrice Elohor Ifie, Pangirayi Tongoona and Eric Yirenkyi Danquah
Genes 2022, 13(2), 349; https://doi.org/10.3390/genes13020349 - 15 Feb 2022
Cited by 7 | Viewed by 2828
Abstract
Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined [...] Read more.
Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers. Full article
(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)
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15 pages, 2212 KiB  
Article
Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam (Dioscorea alata)
by Paterne Angelot Agre, Kwabena Darkwa, Bunmi Olasanmi, Olufisayo Kolade, Pierre Mournet, Ranjana Bhattacharjee, Antonio Lopez-Montes, David De Koeyer, Patrick Adebola, Lava Kumar, Robert Asiedu and Asrat Asfaw
Genes 2022, 13(2), 347; https://doi.org/10.3390/genes13020347 - 14 Feb 2022
Cited by 4 | Viewed by 2880
Abstract
Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop [...] Read more.
Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop durable-resistant cultivars for sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the Genotyping by Sequencing (GBS) platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3184 polymorphic Single Nucleotide Polymorphism (NSP) markers well distributed across the genome, covering 1460.94 cM total length. On average, 163 SNP markers were mapped per chromosome with 0.58 genetic distances between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on three chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam. Full article
(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)
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19 pages, 16013 KiB  
Article
Genomic Analysis of Resistance to Fall Armyworm (Spodoptera frugiperda) in CIMMYT Maize Lines
by Isaac Kamweru, Bruce Y. Anani, Yoseph Beyene, Dan Makumbi, Victor O. Adetimirin, Boddupalli M. Prasanna and Manje Gowda
Genes 2022, 13(2), 251; https://doi.org/10.3390/genes13020251 - 28 Jan 2022
Cited by 12 | Viewed by 3192
Abstract
The recent invasion, rapid spread, and widescale destruction of the maize crop by the fall armyworm (FAW; Spodoptera frugiperda (J.E. Smith)) is likely to worsen the food insecurity situation in Africa. In the present study, a set of 424 maize lines were screened [...] Read more.
The recent invasion, rapid spread, and widescale destruction of the maize crop by the fall armyworm (FAW; Spodoptera frugiperda (J.E. Smith)) is likely to worsen the food insecurity situation in Africa. In the present study, a set of 424 maize lines were screened for their responses to FAW under artificial infestation to dissect the genetic basis of resistance. All lines were evaluated for two seasons under screen houses and genotyped with the DArTseq platform. Foliar damage was rated on a scale of 1 (highly resistant) to 9 (highly susceptible) and scored at 7, 14, and 21 days after artificial infestation. Analyses of variance revealed significant genotypic and genotype by environment interaction variances for all traits. Heritability estimates for leaf damage scores were moderately high and ranged from 0.38 to 0.58. Grain yield was negatively correlated with a high magnitude to foliar damage scores, ear rot, and ear damage traits. The genome-wide association study (GWAS) revealed 56 significant marker–trait associations and the predicted functions of the putative candidate genes varied from a defense response to several genes of unknown function. Overall, the study revealed that native genetic resistance to FAW is quantitative in nature and is controlled by many loci with minor effects. Full article
(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)
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20 pages, 3674 KiB  
Article
Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family
by Ashley G. Yow, Hamed Bostan, Raúl Castanera, Valentino Ruggieri, Molla F. Mengist, Julien Curaba, Roberto Young, Nicholas Gillitt and Massimo Iorizzo
Genes 2022, 13(1), 52; https://doi.org/10.3390/genes13010052 - 24 Dec 2021
Cited by 4 | Viewed by 4175
Abstract
Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and [...] Read more.
Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple. Full article
(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)
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