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

Deadline for manuscript submissions: closed (25 April 2022) | Viewed by 33921

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Special Issue Editors

Dr. Kassa Semagn

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Guest Editor

Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB T6G2R3, Canada
Interests: genetic diversity studies; genomics of genebanks; germplasm conservation; gene and QTL discovery; germplasm enhancement (pre-breeding); marker-assisted selection; genomic selection
Special Issues, Collections and Topics in MDPI journals

Dr. Antonio Costa De Oliveira

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Crop Science Department, Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, Brazil
Interests: genomics; plants; cereals; abiotic stresses

Dr. Bhoja Raj Basnet

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Guest Editor

Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), El Batán 56237, Mexico
Interests: breeding and genetics; genomics; hybrid wheat; host plant interaction; wheat rust; disease resistance; genomic prediction; marker assisted selection; GWAS

Special Issue Information

Dear Colleagues,

Nearly half of the genetic gain under farmers’ fields has been estimated to be due to changes in the genetic makeup of crops through breeding, which depends on the availability of good germplasm, access to modern breeding tools, the selection intensity, trait complexity (heritability), and generation interval (number of cycles completed per year). Breeders have access to thousands of collections (breeding lines, wild relatives, landraces, obsolete and modern varieties) stored across numerous genebanks, but they only exploit the genetic potential of a very tiny fraction of the genetic diversity of a given species. This Special Issue will feature original research articles, literature reviews, and opinion papers on topics including but not limited to: (1) germplasm characterization and subsetting (core and mini-cores) using high-density molecular markers and next-generation sequencing technologies; (2) development and implementation of genotyping quality control and quality asurance; (3) gene and QTL discovery, fine mapping, and validation in bi-parental populations and genome-wide association mapping panels; (4) pre-breeding (germplasm enhancement); (5) developing improved germplasm using modern breeding methods; (6) estimating genetic gains. This Special Issue aims to provide novel insights and new perspectives on accelerating plant breeding to develop abiotic and biotic tolerant/resistant germplasm for the changing climate.

Dr. Kassa Semagn
Dr. Antonio Costa De Oliveira
Dr. Bhoja Raj Basnet
Guest Editors

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Keywords

abiotic tolerance
core
mini-core
disease resistance
end-use quality traits
gene discovery
genetic diversity
genetic mapping
genomics of genebanks
germplasm conservation
germplasm enhancement
marker-assisted selection
genomic selection
genetic gain
molecular breeding
selective sweep analysis
subsetting

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Published Papers (8 papers)

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Research

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20 pages, 11746 KiB

Open AccessArticle

Identification of Spring Wheat with Superior Agronomic Performance under Contrasting Nitrogen Managements Using Linear Phenotypic Selection Indices

by Muhammad Iqbal, Kassa Semagn, J. Jesus Céron-Rojas, José Crossa, Diego Jarquin, Reka Howard, Brian L. Beres, Klaus Strenzke, Izabela Ciechanowska and Dean Spaner

Plants 2022, 11(14), 1887; https://doi.org/10.3390/plants11141887 - 20 Jul 2022

Cited by 1 | Viewed by 2192

Abstract

Both the Linear Phenotypic Selection Index (LPSI) and the Restrictive Linear Phenotypic Selection Index (RLPSI) have been widely used to select parents and progenies, but the effect of economic weights on the selection parameters (the expected genetic gain, response to selection, and the correlation between the indices and genetic merits) have not been investigated in detail. Here, we (i) assessed combinations of 2304 economic weights using four traits (maturity, plant height, grain yield and grain protein content) recorded under four organically (low nitrogen) and five conventionally (high nitrogen) managed environments, (ii) compared single-trait and multi-trait selection indices (LPSI vs. RLPSI by imposing restrictions to the expected genetic gain of either yield or grain protein content), and (iii) selected a subset of about 10% spring wheat cultivars that performed very well under organic and/or conventional management systems. The multi-trait selection indices, with and without imposing restrictions, were superior to single trait selection. However, the selection parameters differed quite a lot depending on the economic weights, which suggests the need for optimizing the weights. Twenty-two of the 196 cultivars that showed superior performance under organic and/or conventional management systems were consistently selected using all five of the selected economic weights, and at least two of the selection scenarios. The selected cultivars belonged to the Canada Western Red Spring (16 cultivars), the Canada Northern Hard Red (3), and the Canada Prairie Spring Red (3), and required 83–93 days to maturity, were 72–100 cm tall, and produced from 4.0 to 6.2 t ha⁻¹ grain yield with 14.6–17.7% GPC. The selected cultivars would be highly useful, not only as potential trait donors for breeding under an organic management system, but also for other studies, including nitrogen use efficiency. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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16 pages, 2488 KiB

Open AccessArticle

New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species

by Alexander A. Gnutikov, Nikolai N. Nosov, Igor G. Loskutov, Elena V. Blinova, Viktoria S. Shneyer, Nina S. Probatova and Alexander V. Rodionov

Plants 2022, 11(9), 1103; https://doi.org/10.3390/plants11091103 - 19 Apr 2022

Cited by 2 | Viewed by 2090

Abstract

We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4–49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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14 pages, 4236 KiB

Open AccessArticle

Genetic Diversity, Population Structure and Linkage Disequilibrium Analyses in Tropical Maize Using Genotyping by Sequencing

by Bhupender Kumar, Sujay Rakshit, Sonu Kumar, Brijesh Kumar Singh, Chayanika Lahkar, Abhishek Kumar Jha, Krishan Kumar, Pardeep Kumar, Mukesh Choudhary, Shyam Bir Singh, John J. Amalraj, Bhukya Prakash, Rajesh Khulbe, Mehar Chand Kamboj, Neeraja N. Chirravuri and Firoz Hossain

Plants 2022, 11(6), 799; https://doi.org/10.3390/plants11060799 - 17 Mar 2022

Cited by 13 | Viewed by 3705

Abstract

Several maize breeding programs in India have developed numerous inbred lines but the lines have not been characterized using high-density molecular markers. Here, we studied the molecular diversity, population structure, and linkage disequilibrium (LD) patterns in a panel of 314 tropical normal corn, two sweet corn, and six popcorn inbred lines developed by 17 research centers in India, and 62 normal corn from the International Maize and Wheat Improvement Center (CIMMYT). The 384 inbred lines were genotyped with 60,227 polymorphic single nucleotide polymorphisms (SNPs). Most of the pair-wise relative kinship coefficients (58.5%) were equal or close to 0, which suggests the lack of redundancy in the genomic composition in the majority of inbred lines. Genetic distance among most pairs of lines (98.3%) varied from 0.20 to 0.34 as compared with just 1.7% of the pairs of lines that differed by <0.20, which suggests greater genetic variation even among sister lines. The overall average of 17% heterogeneity was observed in the panel indicated the need for further inbreeding in the high heterogeneous genotypes. The mean nucleotide diversity and frequency of polymorphic sites observed in the panel were 0.28 and 0.02, respectively. The model-based population structure, principal component analysis, and phylogenetic analysis revealed three to six groups with no clear patterns of clustering by centers-wise breeding lines, types of corn, kernel characteristics, maturity, plant height, and ear placement. However, genotypes were grouped partially based on their source germplasm from where they derived. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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11 pages, 1164 KiB

Open AccessArticle

Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1

by Yuya Liang, Shichen Wang, Chersty L. Harper, Nithya K. Subramanian, Rodante E. Tabien, Charles D. Johnson, Julia Bailey-Serres and Endang M. Septiningsih

Plants 2021, 10(12), 2740; https://doi.org/10.3390/plants10122740 - 13 Dec 2021

Viewed by 4401

Abstract

Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s). Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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12 pages, 2487 KiB

Open AccessArticle

Formation of Potential Heterotic Groups of Oat Using Variation at Microsatellite Loci

by Michaela Havrlentová, Katarína Ondreičková, Peter Hozlár, Veronika Gregusová, Daniel Mihálik and Ján Kraic

Plants 2021, 10(11), 2462; https://doi.org/10.3390/plants10112462 - 15 Nov 2021

Cited by 3 | Viewed by 2134

Abstract

An evaluation of polymorphism at the microsatellite loci was applied in distinguishing 85 oat (Avena sativa L.) genotypes selected from the collection of genetic resources. The set of genotypes included oats with white, yellow, and brown seeds as well as a subgroup of naked oat (Avena sativa var. nuda Koern). Variation at these loci was used to form potential heterotic groups potentially used in the oat breeding program. Seven from 20 analyzed microsatellite loci revealed polymorphism. Altogether, 35 microsatellite alleles were detected (2–10 per locus). Polymorphic patterns completely differentiated all genotypes within the subgroups of white, brown, and naked oats, respectively. Only within the greatest subgroup of yellow genotypes, four pairs of genotypes remained unseparated. Genetic differentiation between the oat subgroups allowed the formation of seven potential heterotic groups using the STRUCTURE analysis. The overall value of the fixation index (F_st) suggested a high genetic differentiation between the subgroups and validated a heterotic grouping. This approach can be implemented as a simple predictor of heterosis in parental crosses prior to extensive field testing or development and implementation of more accurate genomic selection. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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23 pages, 1930 KiB

Open AccessArticle

Physical Mapping of QTL in Four Spring Wheat Populations under Conventional and Organic Management Systems. I. Earliness

by Kassa Semagn, Muhammad Iqbal, Hua Chen, Enid Perez-Lara, Darcy H. Bemister, Rongrong Xiang, Jun Zou, Muhammad Asif, Atif Kamran, Amidou N’Diaye, Harpinder Randhawa, Curtis Pozniak and Dean Spaner

Plants 2021, 10(5), 853; https://doi.org/10.3390/plants10050853 - 23 Apr 2021

Cited by 11 | Viewed by 2949

Abstract

In previous studies, we reported quantitative trait loci (QTL) associated with the heading, flowering, and maturity time in four hard red spring wheat recombinant inbred line (RIL) populations but the results are scattered in population-specific genetic maps, which is challenging to exploit efficiently in breeding. Here, we mapped and characterized QTL associated with these three earliness traits using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. Our data consisted of (i) 6526 single nucleotide polymorphisms (SNPs) and two traits evaluated at five conventionally managed environments in the ‘Cutler’ × ‘AC Barrie’ population; (ii) 3158 SNPs and two traits evaluated across three organic and seven conventional managements in the ‘Attila’ × ‘CDC Go’ population; (iii) 5731 SilicoDArT and SNP markers and the three traits evaluated at four conventional and organic management systems in the ‘Peace’ × ‘Carberry’ population; and (iv) 1058 SNPs and two traits evaluated across two conventionally and organically managed environments in the ‘Peace’ × ‘CDC Stanley’ population. Using composite interval mapping, the phenotypic data across all environments, and the IWGSC RefSeq v2.0 physical maps, we identified a total of 44 QTL associated with days to heading (11), flowering (10), and maturity (23). Fifteen of the 44 QTL were common to both conventional and organic management systems, and the remaining QTL were specific to either the conventional (21) or organic (8) management systems. Some QTL harbor known genes, including the Vrn-A1, Vrn-B1, Rht-A1, and Rht-B1 that regulate photoperiodism, flowering time, and plant height in wheat, which lays a solid basis for cloning and further characterization. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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Review

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26 pages, 1177 KiB

Open AccessReview

Applications of In Vitro Tissue Culture Technologies in Breeding and Genetic Improvement of Wheat

by Akila Wijerathna-Yapa, Vinita Ramtekey, Buddhini Ranawaka and Bhoja Raj Basnet

Plants 2022, 11(17), 2273; https://doi.org/10.3390/plants11172273 - 31 Aug 2022

Cited by 13 | Viewed by 8195

Abstract

Sources of new genetic variability have been limited to existing germplasm in the past. Wheat has been studied extensively for various agronomic traits located throughout the genome. The large size of the chromosomes and the ability of its polyploid genome to tolerate the addition or loss of chromosomes facilitated rapid progress in the early study of wheat genetics using cytogenetic techniques. At the same time, its large genome size has limited the progress in genetic characterization studies focused on diploid species, with a small genome and genetic engineering procedures already developed. Today, the genetic transformation and gene editing procedures offer attractive alternatives to conventional techniques for breeding wheat because they allow one or more of the genes to be introduced or altered into an elite cultivar without affecting its genetic background. Recently, significant advances have been made in regenerating various plant tissues, providing the essential basis for regenerating transgenic plants. In addition, Agrobacterium-mediated, biolistic, and in planta particle bombardment (iPB) gene delivery procedures have been developed for wheat transformation and advanced transgenic wheat development. As a result, several useful genes are now available that have been transferred or would be helpful to be transferred to wheat in addition to the current traditional effort to improve trait values, such as resistance to abiotic and biotic factors, grain quality, and plant architecture. Furthermore, the in planta genome editing method will significantly contribute to the social implementation of genome-edited crops to innovate the breeding pipeline and leverage unique climate adaptations. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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22 pages, 1188 KiB

Open AccessReview

Opportunities for Improving Waterlogging Tolerance in Cereal Crops—Physiological Traits and Genetic Mechanisms

by Cen Tong, Camilla Beate Hill, Gaofeng Zhou, Xiao-Qi Zhang, Yong Jia and Chengdao Li

Plants 2021, 10(8), 1560; https://doi.org/10.3390/plants10081560 - 29 Jul 2021

Cited by 43 | Viewed by 6620

Abstract

Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley. Full article

(This article belongs to the Special Issue Cereals Genetic Resources and Improvement)

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