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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 December 2022) | Viewed by 11859

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Prof. Dr. Agata Gadaleta

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Department of Agriculture & Environmental Sciences, University of Bari Aldo Moro, Via G Amendola 165-A, I-70126 Bari, Italy
Interests: wheat; molecular marker; QTL analysis; genetic map; nitrogen metabolism; genetic trasformation; wheat quality; biotic stress tolerance
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Dr. José Miguel Soriano

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Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), 25198 Lleida, Spain
Interests: plant breeding; genomics; marker-assisted selection; gene discovery
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Special Issue Information

Dear Colleagues,

The Special Issue will focus on recent advances in “New Breeding Technologies in Grasses”. We welcome novel research and reviews covering all related topics, including new marker technologies, fine mapping and gene discovery, speed breeding, cisgenesis, gene editing, reverse breeding, DNA methylation, and oligonucleotide-directed mutagenesis (ODM). This issue will present a good picture of the state-of-the-art and potential future of breeding approaches.

Plant breeding is continuously evolving to develop new cultivars with the desired traits in the most efficient way. This progress has been particularly significant from the 1980s, when agriculture and plant breeding experienced a great impulse due to the development of the molecular biology. This advancement allowed plant scientists and breeders to understand the genetic basis of complex traits leading to their manipulation to produce improved cultivars. New plant-breeding techniques (NBT) report economic advantages as the time to obtain a new cultivar is reduced. Overall, the NBT permits breeders to introduce a target trait in an efficient and precise way, thus accelerating the selection procedure.

Prof. Dr. Agata Gadaleta
Dr. José Miguel Soriano
Guest Editors

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Published Papers (6 papers)

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Editorial

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3 pages, 192 KiB

Open AccessEditorial

New Breeding Technologies in Grasses

by Agata Gadaleta and Jose Miguel Soriano

Int. J. Mol. Sci. 2023, 24(8), 7295; https://doi.org/10.3390/ijms24087295 - 14 Apr 2023

Viewed by 1501

Abstract

Plant breeding is continuously evolving to develop new cultivars with the desired traits in the most efficient way [...] Full article

(This article belongs to the Special Issue New Breeding Technologies in Grasses)

Research

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19 pages, 1391 KiB

Open AccessArticle

Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS

by Venkata Rami Reddy Yannam, Rubén Rufo, Ilaria Marcotuli, Agata Gadaleta, Marta S. Lopes and Jose Miguel Soriano

Int. J. Mol. Sci. 2023, 24(2), 1700; https://doi.org/10.3390/ijms24021700 - 15 Jan 2023

Cited by 3 | Viewed by 1593

Abstract

Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar ‘Chinese Spring’ detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci. Full article

(This article belongs to the Special Issue New Breeding Technologies in Grasses)

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18 pages, 6514 KiB

Open AccessArticle

Molecular Mechanism of Cold Tolerance of Centipedegrass Based on the Transcriptome

by Yingjie Liu, Yi Xiong, Junming Zhao, Shiqie Bai, Daxu Li, Limin Chen, Junjie Feng, Yingzhu Li, Xiao Ma and Jianbo Zhang

Int. J. Mol. Sci. 2023, 24(2), 1265; https://doi.org/10.3390/ijms24021265 - 9 Jan 2023

Cited by 7 | Viewed by 2209

Abstract

Low temperature is an important limiting factor in the environment that affects the distribution, growth and development of warm-season grasses. Transcriptome sequencing has been widely used to mine candidate genes under low-temperature stress and other abiotic stresses. However, the molecular mechanism of centipedegrass in response to low-temperature stress was rarely reported. To understand the molecular mechanism of centipedegrass in response to low-temperature stress, we measured physiological indicators and sequenced the transcriptome of centipedegrass under different stress durations. Under cold stress, the SS content and APX activity of centipedegrass increased while the SOD activity decreased; the CAT activity, POD activity and flavonoid content first increased and then decreased; and the GSH-Px activity first decreased and then increased. Using full-length transcriptome and second-generation sequencing, we obtained 38.76 G subreads. These reads were integrated into 177,178 isoforms, and 885 differentially expressed transcripts were obtained. The expression of AUX_IAA and WRKY transcription factors and HSF transcription-influencing factors increased during cold stress. Through KEGG enrichment analysis, we determined that arginine and proline metabolism, plant circadian rhythm, plant hormone signal transduction and the flavonoid biosynthesis pathways played important roles in the cold stress resistance of centipedegrass. In addition, by using weighted gene coexpression network analysis (WGCNA), we determined that the turquoise module was significantly correlated with SS content and APX activity, while the blue module was significantly negatively correlated with POD and CAT activity. This paper is the first to report the response of centipedegrass to cold stress at the transcriptome level. Our results help to clarify the molecular mechanisms underlying the cold tolerance of warm-season grasses. Full article

(This article belongs to the Special Issue New Breeding Technologies in Grasses)

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20 pages, 2580 KiB

Open AccessArticle

Genome-Wide Association Analysis of Senescence-Related Traits in Maize

by Venkata Rami Reddy Yannam, Marlon Caicedo, Rosa Ana Malvar and Bernardo Ordás

Int. J. Mol. Sci. 2022, 23(24), 15897; https://doi.org/10.3390/ijms232415897 - 14 Dec 2022

Cited by 3 | Viewed by 1621

Abstract

Senescence is a programmed process that involves the destruction of the photosynthesis apparatus and the relocation of nutrients to the grain. Identifying senescence-associated genes is essential to adapting varieties for the duration of the cultivation cycle. A genome-wide association study (GWAS) was performed using 400 inbred maize lines with 156,164 SNPs to study the genetic architecture of senescence-related traits and their relationship with agronomic traits. We estimated the timing of senescence to be 45 days after anthesis in the whole plant and specifically in the husks. A list of genes identified in a previous RNAseq experiment as involved in senescence (core senescence genes) was used to propose candidate genes in the vicinity of the significant SNPs. Forty-six QTLs of moderate to high effect were found for senescence traits, including specific QTLs for husk senescence. The allele that delayed senescence primarily increased grain yield and moisture. Seven and one significant SNPs were found in the coding and promoter regions of eight core senescence genes, respectively. These genes could be potential candidates for generating a new variation by genome editing for functional analysis and breeding purposes, particularly Zm00001d014796, which could be responsible for a QTL of senescence found in multiple studies. Full article

(This article belongs to the Special Issue New Breeding Technologies in Grasses)

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19 pages, 1563 KiB

Open AccessArticle

Identification of New QTLs for Dietary Fiber Content in Aegilops biuncialis

by László Ivanizs, Ilaria Marcotuli, Marianna Rakszegi, Balázs Kalapos, Kitti Szőke-Pázsi, András Farkas, Edina Türkösi, Eszter Gaál, Klaudia Kruppa, Péter Kovács, Éva Darkó, Éva Szakács, Mahmoud Said, Petr Cápal, Jaroslav Doležel, Agata Gadaleta and István Molnár

Int. J. Mol. Sci. 2022, 23(7), 3821; https://doi.org/10.3390/ijms23073821 - 30 Mar 2022

Cited by 6 | Viewed by 2044

Abstract

Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass Aegilops biuncialis has high β-glucan content, which makes it an attractive gene source to develop wheat lines with modified fiber composition. In order to support introgression breeding, this work examined genetic variability in grain β-glucan, pentosan, and protein content in a collection of Ae. biuncialis. A large variation in grain protein and edible fiber content was revealed, reflecting the origin of Ae. biuncialis accessions from different eco-geographical habitats. Association analysis using DArTseq-derived SNPs identified 34 QTLs associated with β-glucan, pentosan, water-extractable pentosan, and protein content. Mapping the markers to draft chromosome assemblies of diploid progenitors of Ae. biuncialis underlined the role of genes on chromosomes 1M^b, 4M^b, and 5M^b in the formation of grain β-glucan content, while other QTLs on chromosome groups 3, 6, and 1 identified genes responsible for total- and water-extractable pentosan content. Functional annotation of the associated marker sequences identified fourteen genes, nine of which were identified in other monocots. The QTLs and genes identified in the present work are attractive targets for chromosome-mediated gene transfer to improve the health-promoting properties of wheat-derived foods. Full article

(This article belongs to the Special Issue New Breeding Technologies in Grasses)

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Review

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20 pages, 885 KiB

Open AccessReview

Using Genomic Selection to Develop Performance-Based Restoration Plant Materials

by Thomas A. Jones, Thomas A. Monaco, Steven R. Larson, Erik P. Hamerlynck and Jared L. Crain

Int. J. Mol. Sci. 2022, 23(15), 8275; https://doi.org/10.3390/ijms23158275 - 27 Jul 2022

Cited by 5 | Viewed by 2126

Abstract

Effective native plant materials are critical to restoring the structure and function of extensively modified ecosystems, such as the sagebrush steppe of North America’s Intermountain West. The reestablishment of native bunchgrasses, e.g., bluebunch wheatgrass (Pseudoroegneria spicata [Pursh] À. Löve), is the first step for recovery from invasive species and frequent wildfire and towards greater ecosystem resiliency. Effective native plant material exhibits functional traits that confer ecological fitness, phenotypic plasticity that enables adaptation to the local environment, and genetic variation that facilitates rapid evolution to local conditions, i.e., local adaptation. Here we illustrate a multi-disciplinary approach based on genomic selection to develop plant materials that address environmental issues that constrain local populations in altered ecosystems. Based on DNA sequence, genomic selection allows rapid screening of large numbers of seedlings, even for traits expressed only in more mature plants. Plants are genotyped and phenotyped in a training population to develop a genome model for the desired phenotype. Populations with modified phenotypes can be used to identify plant syndromes and test basic hypotheses regarding relationships of traits to adaptation and to one another. The effectiveness of genomic selection in crop and livestock breeding suggests this approach has tremendous potential for improving restoration outcomes for species such as bluebunch wheatgrass. Full article

(This article belongs to the Special Issue New Breeding Technologies in Grasses)

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