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Agronomy
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Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits
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Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits

A special issue of Agronomy (ISSN 2073-4395).

Deadline for manuscript submissions: closed (1 December 2014) | Viewed by 35789

Special Issue Editor

Dr. Bertrand Hirel

E-Mail Website
Guest Editor
Adaptation des Plantes à leur Environnement, Unité de Recherche 511, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Route de Saint-Cyr, F-78026 Versailles Cedex, France
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Both from an agronomic and economic point of view, the main driver for crop improvement over the last century has been the yield. Recently, the rate of improvement of yield and grain protein content has accelerated, due primarily to the introduction of an increasingly scientific approach to plant breeding. In particular, quantitative genetics, through the use of DNA markers and the detection of quantitative trait loci, has been the main approach for the identification of chromosomal regions together with key regulatory or structural candidate genes involved in the expression of complex agronomic traits such as yield. The identification of such chromosomal regions and genes, involved in the control of yield and grain quality, should provide the basis for developing marker-assisted selection strategies. This will allow breeders to exploit all the possibilities offered by genetics, including natural variability, mutagenesis and genetic manipulation. Among these possibilities, validation of candidate genes putatively involved in the control of yield has been extensively developed using transgenic and mutagenesis technologies. In addition, studies have examined the relationship between allelic polymorphism and the trait of interest, either at the single gene or genome-wide level. Positional cloning is another alternative strategy that can be used to focus on the chromosomal regions controlling yield, and this ultimately facilitates access to a single gene. Thus, the next major challenge for plant biologists and breeders will consist of taking advantage of these genetic and molecular marker technologies to increase crop yield to feed the world.

Dr. Bertrand Hirel
Guest Editor

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Keywords

  • association genetics
  • breeding
  • genetic engineering
  • molecular markers
  • mutants
  • quantitative trait loci
  • yield

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Published Papers (5 papers)

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28 pages, 9457 KiB  
Article
Genomic Regions for Embryo Size and Early Vigour in Multiple Wheat (Triticum aestivum L.) Populations
by Chris Moore and Greg Rebetzke
Agronomy 2015, 5(2), 152-179; https://doi.org/10.3390/agronomy5020152 - 5 May 2015
Cited by 20 | Viewed by 7068
Abstract
Greater early vigour has potential for increasing biomass and grain yields of wheat crops in Mediterranean-type environments. Embryo size is an important determinant of early vigour in barley and likely to contribute to greater vigour in wheat. Little is known of the underlying [...] Read more.
Greater early vigour has potential for increasing biomass and grain yields of wheat crops in Mediterranean-type environments. Embryo size is an important determinant of early vigour in barley and likely to contribute to greater vigour in wheat. Little is known of the underlying genetic control for embryo size, or its genetic association with early vigour in wheat. Over 150 doubled-haploid lines in each of three unrelated wheat populations varying for embryo size and early vigour were phenotyped across multiple controlled environments. The Quantitative Trait Locus (QTL) mapping was then undertaken to understand genetic control and chromosomal location of these characteristics. Genotypic variance was large and repeatable for embryo and leaf size (width and length) but not specific leaf area or coleoptile tiller size. Genetic correlations for embryo size with leaf width and area were moderate to strong in size while repeatabilities for embryo size and early vigour were high on a line-mean basis. Multiple genomic regions were identified of commonly small genetic effect for each trait with many of these regions being common across populations. Further, collocation of regions for many traits inferred a common genetic basis for many of these traits. Chromosomes 1B, 5B, 7A and 7D, and the Rht-B1b and Rht-D1b-containing chromosomes 4B and 4D contained QTL for embryo size and leaf width. These studies indicate that while early vigour is a genetically complex trait, the selection of larger embryo progeny can be readily achieved in a wheat breeding program targeting development of high vigour lines. Full article
(This article belongs to the Special Issue Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits)
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9 pages, 4357 KiB  
Article
Detection of NAM-A1 Natural Variants in Bread Wheat Reveals Differences in Haplotype Distribution between a Worldwide Core Collection and European Elite Germplasm
by Fabien Cormier, Mickaël Throude, Catherine Ravel, Jacques Le Gouis, Magalie Leveugle, Stéphane Lafarge, Florence Exbrayat, Nadine Duranton and Sébastien Praud
Agronomy 2015, 5(2), 143-151; https://doi.org/10.3390/agronomy5020143 - 29 Apr 2015
Cited by 24 | Viewed by 7236
Abstract
In wheat, remobilization of nitrogen absorbed before anthesis and regulation of monocarpic senescence is a major issue in breeding for nutrient use efficiency. We identified natural variants of NAM-A1, a gene having the same role as its well-characterized homoeolog NAM-B1, a [...] Read more.
In wheat, remobilization of nitrogen absorbed before anthesis and regulation of monocarpic senescence is a major issue in breeding for nutrient use efficiency. We identified natural variants of NAM-A1, a gene having the same role as its well-characterized homoeolog NAM-B1, a NAC transcription factor associated with senescence kinetics and nutrient remobilization to the grain. Differences in haplotype frequencies between a worldwide core collection and a panel of European elite varieties were assessed and discussed. Moreover, hypotheses for the loss of function of the most common haplotype in elite European germplasm are discussed. Full article
(This article belongs to the Special Issue Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits)
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16 pages, 380 KiB  
Article
The Potential of Lr19 and Bdv2 Translocations to Improve Yield and Disease Resistance in the High Rainfall Wheat Zones of Australia
by Garry Rosewarne, David Bonnett, Greg Rebetzke, Paul Lonergan and Philip J. Larkin
Agronomy 2015, 5(1), 55-70; https://doi.org/10.3390/agronomy5010055 - 16 Feb 2015
Cited by 6 | Viewed by 6976
Abstract
Chromosomal translocations in wheat derived from alien species are a valuable source of genetic diversity that have provided increases in resistance to various diseases and improved tolerance to abiotic stresses in wheat. These alien genomic segments can also affect multiple traits, with a [...] Read more.
Chromosomal translocations in wheat derived from alien species are a valuable source of genetic diversity that have provided increases in resistance to various diseases and improved tolerance to abiotic stresses in wheat. These alien genomic segments can also affect multiple traits, with a concomitant ability to alter yield potential in either a positive or negative fashion. The aim of this work was to characterize the effects on yield of two types of translocations, namely T4-derived translocations from Thinopyrum ponticum, carrying the leaf rust resistance gene Lr19, and the TC14 translocation from Th. intermedium, carrying the barley yellow dwarf virus resistance gene Bdv2, in Australian adapted genetic backgrounds and under Australian conditions. A large range of germplasm was developed by crossing donor sources of the translocations into 24 Australian adapted varieties producing 340 genotypes. Yield trials were conducted in 14 environments to identify effects on yield and yield components. The T4 translocations had a positive effect on yield in one high yielding environment, but negatively affected yield in low-yielding environments. The TC14 translocation was generally benign, however, it was associated with a negative impact on yield and reduced height in two genetic backgrounds. The translocation was also associated with a delayed maturity in several backgrounds. The T4 translocations results were consistent with previously published data, whilst this is the first time that such an investigation has been undertaken on the TC14 translocation. Our data suggests a limited role for each of these translocations in Australia. The T4 translocations may be useful in high yielding environments, such as under irrigation in NSW and in the more productive high rainfall regions of south-eastern Australia. Traits associated with the TC14 translocation, such as BYDV resistance and delayed maturity, would make this translocation useful in BYDV-prone areas that experience a less pronounced terminal drought (e.g., south-eastern Australia). Full article
(This article belongs to the Special Issue Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits)
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23 pages, 531 KiB  
Article
Genetic Dissection of QTL Associated with Grain Yield in Diverse Environments
by Junli Zhang, Jianli Chen, Chenggen Chu, Weidong Zhao, Justin Wheeler, Edward J. Souza and Robert S. Zemetra
Agronomy 2014, 4(4), 556-578; https://doi.org/10.3390/agronomy4040556 - 5 Dec 2014
Cited by 12 | Viewed by 6904
Abstract
Wheat (Triticum aestivum L.) breeding programs strive to increase grain yield; however, the progress is hampered due to its quantitative inheritance, low heritability, and confounding environmental effects. In the present study, a winter wheat population of 159 recombinant inbred lines (RILs) was [...] Read more.
Wheat (Triticum aestivum L.) breeding programs strive to increase grain yield; however, the progress is hampered due to its quantitative inheritance, low heritability, and confounding environmental effects. In the present study, a winter wheat population of 159 recombinant inbred lines (RILs) was evaluated in six trials under rainfed, terminal drought, and fully-irrigated conditions, over four years. Quantitative trait locus/loci (QTL) mapping was conducted for grain yield main effect (GY) and the genotype × environment interaction (GEI) effect. A total of 17 QTL were associated with GY and 13 QTL associated with GEI, and nine QTL were mapped in the flanking chromosomal regions for both GY and GEI. One major QTL Q.Gy.ui-1B.2, explaining up to 22% of grain yield, was identified in all six trials. Besides the additive effect of QTL associated with GY, interactions among QTL (QTL × QTL interaction), QTL × environment, and QTL × QTL × environment were also observed. When combining the interaction effects, QTL Q.Gy.ui-1B.2 along with other QTL explained up to 52% of the variation in grain yield over the six trials. This study suggests that QTL mapping of complex traits such as grain yield should include interaction effects of QTL and environments in marker-assisted selection. Full article
(This article belongs to the Special Issue Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits)
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8 pages, 281 KiB  
Article
Candidate Gene Identification for a Lethal Chlorophyll-Deficient Mutant in Soybean
by Sam Reed, Taylor Atkinson, Carly Gorecki, Katherine Espinosa, Sarah Przybylski, Alcira Susana Goggi, Reid G. Palmer and Devinder Sandhu
Agronomy 2014, 4(4), 462-469; https://doi.org/10.3390/agronomy4040462 - 31 Oct 2014
Cited by 14 | Viewed by 6874
Abstract
Chlorophyll-deficient mutants have been studied persistently to understand genetic mechanisms controlling metabolic pathways. A spontaneous chlorophyll-deficient lethal mutant was observed in self-pollinated progeny of a soybean cultivar “BSR 101”. Observed segregation patterns indicated single-gene recessive inheritance for this lethal-yellow mutant. The objectives of [...] Read more.
Chlorophyll-deficient mutants have been studied persistently to understand genetic mechanisms controlling metabolic pathways. A spontaneous chlorophyll-deficient lethal mutant was observed in self-pollinated progeny of a soybean cultivar “BSR 101”. Observed segregation patterns indicated single-gene recessive inheritance for this lethal-yellow mutant. The objectives of this investigation were to develop a genetic linkage map of the region containing the lethal-yellow (YL_PR350) gene and identify putative candidate genes for this locus. The YL_PR350 gene was mapped to chromosome 15 and is flanked by BARCSOYSSR_15_1591 and BARCSOYSSR_15_1597. This region physically spans ~153 kb and there are 14 predicted genes that lie in this region. The predicted gene Glyma.15g275900 is an excellent candidate for the YL_PR350 gene as it is homologous to an Arabidopsis gene, At3g08010, which codes for a chloroplast-localized protein (ATAB2) involved in the biogenesis of Photosystem I and II. This thylakoid membrane protein is crucial for photosynthesis in Arabidopsis. Future characterization of the candidate gene may enhance our knowledge about photosynthesis, a complex metabolic process critical for sustainability of plants. Full article
(This article belongs to the Special Issue Genomic and Molecular Marker Technologies to Identify Yield-Determining Traits)
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