International Journal of Molecular Sciences

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4 pages, 157 KiB

Open AccessEditorial

Wheat Breeding through Genetic and Physical Mapping

by Agata Gadaleta

Int. J. Mol. Sci. 2020, 21(22), 8739; https://doi.org/10.3390/ijms21228739 - 19 Nov 2020

Cited by 1 | Viewed by 1589

Abstract

The Special Issue of “Wheat breeding through genetic and physical mapping” aimed to collect recent advances in research on the genetic and physical mapping of quantitative trait loci (QTLs), candidate genes and regulatory sequences involved in the control of wheat’s important agronomic traits, [...] Read more.

The Special Issue of “Wheat breeding through genetic and physical mapping” aimed to collect recent advances in research on the genetic and physical mapping of quantitative trait loci (QTLs), candidate genes and regulatory sequences involved in the control of wheat’s important agronomic traits, such as grain yield and quality, biotic and abiotic stress resistance [...] Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

Research

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12 pages, 5910 KiB

Open AccessArticle

Genetic Mapping of ms1s, a Recessive Gene for Male Sterility in Common Wheat

by Wenlong Yang, Yafei Li, Linhe Sun, Muhammad Shoaib, Jiazhu Sun, Dongzhi Wang, Xin Li, Dongcheng Liu, Kehui Zhan and Aimin Zhang

Int. J. Mol. Sci. 2021, 22(16), 8541; https://doi.org/10.3390/ijms22168541 - 09 Aug 2021

Cited by 5 | Viewed by 1886

Abstract

The utilization of heterosis is an important way to improve wheat yield, and the production of wheat hybrid seeds mainly relies on male-sterile lines. Male sterility in line 15 Fan 03 derived from a cross of 72,180 and Xiaoyan 6 is controlled by [...] Read more.

The utilization of heterosis is an important way to improve wheat yield, and the production of wheat hybrid seeds mainly relies on male-sterile lines. Male sterility in line 15 Fan 03 derived from a cross of 72,180 and Xiaoyan 6 is controlled by a single recessive gene. The gene was mapped to the distal region of chromosome 4BS in a genetic interval of 1.4 cM and physical distance of 6.57 Mb between SSR markers Ms4BS42 and Ms4BS199 using an F₂ population with 1205 individuals. Sterile individuals had a deletion of 4.57 Mb in the region presumed to carry the Ms1 locus. The allele for sterility was therefore named ms1s. Three CAPS markers were developed and verified from the region upstream of the deleted fragment and can be used for ms1s marker-assisted selection in wheat hybrid breeding. This work will enrich the utilization of male sterility genetic resources. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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17 pages, 2495 KiB

Open AccessArticle

Adaptive Traits to Improve Durum Wheat Yield in Drought and Crown Rot Environments

by Samir Alahmad, Yichen Kang, Eric Dinglasan, Elisabetta Mazzucotelli, Kai P. Voss-Fels, Jason A. Able, Jack Christopher, Filippo M. Bassi and Lee T. Hickey

Int. J. Mol. Sci. 2020, 21(15), 5260; https://doi.org/10.3390/ijms21155260 - 24 Jul 2020

Cited by 20 | Viewed by 4505

Abstract

Durum wheat (Triticum turgidum L. ssp. durum) production can experience significant yield losses due to crown rot (CR) disease. Losses are usually exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR, and resistant germplasm is [...] Read more.

Durum wheat (Triticum turgidum L. ssp. durum) production can experience significant yield losses due to crown rot (CR) disease. Losses are usually exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR, and resistant germplasm is not currently available in elite breeding pools. We hypothesize that deploying physiological traits for drought adaptation, such as optimal root system architecture to reduce water stress, might minimize losses due to CR infection. This study evaluated a subset of lines from a nested association mapping population for stay-green traits, CR incidence and yield in field experiments as well as root traits under controlled conditions. Weekly measurements of normalized difference vegetative index (NDVI) in the field were used to model canopy senescence and to determine stay-green traits for each genotype. Genome-wide association studies using DArTseq molecular markers identified quantitative trait loci (QTLs) on chromosome 6B (qCR-6B) associated with CR tolerance and stay-green. We explored the value of qCR-6B and a major QTL for root angle QTL qSRA-6A using yield datasets from six rainfed environments, including two environments with high CR disease pressure. In the absence of CR, the favorable allele for qSRA-6A provided an average yield advantage of 0.57 t·ha⁻¹, whereas in the presence of CR, the combination of favorable alleles for both qSRA-6A and qCR-6B resulted in a yield advantage of 0.90 t·ha⁻¹. Results of this study highlight the value of combining above- and belowground physiological traits to enhance yield potential. We anticipate that these insights will assist breeders to design improved durum varieties that mitigate production losses due to water deficit and CR. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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13 pages, 2212 KiB

Open AccessArticle

Detection of Genomic Regions Associated with Resistance to Stem Rust in Russian Spring Wheat Varieties and Breeding Germplasm

by Irina N. Leonova, Ekaterina S. Skolotneva, Elena A. Orlova, Olga A. Orlovskaya and Elena A. Salina

Int. J. Mol. Sci. 2020, 21(13), 4706; https://doi.org/10.3390/ijms21134706 - 01 Jul 2020

Cited by 13 | Viewed by 2973

Abstract

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is a dangerous disease of common wheat worldwide. Development and cultivation of the varieties with genetic resistance is one of the most effective and environmentally important ways for protection of wheat against fungal [...] Read more.

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is a dangerous disease of common wheat worldwide. Development and cultivation of the varieties with genetic resistance is one of the most effective and environmentally important ways for protection of wheat against fungal pathogens. Field phytopathological screening and genome-wide association study (GWAS) were used for assessment of the genetic diversity of a collection of spring wheat genotypes on stem rust resistance loci. The collection consisting of Russian varieties of spring wheat and introgression lines with alien genetic materials was evaluated over three seasons (2016, 2017 and 2018) for resistance to the native population of stem rust specific to the West Siberian region of Russia. The results indicate that most varieties displayed from moderate to high levels of susceptibility to P. graminis; 16% of genotypes had resistance or immune response. In total, 13,006 single-nucleotide polymorphism (SNP) markers obtained from the Infinium 15K array were used to perform genome-wide association analysis. GWAS detected 35 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1A, 2A, 2B, 3B, 5A, 5B, 6A, 7A and 7B. The most significant associations were found on chromosomes 7A and 6A where known resistance genes Sr25 and Sr6Ai = 2 originated from Thinopyrum ssp. are located. Common wheat lines containing introgressed fragments from Triticum timopheevii and Triticum kiharae were found to carry Sr36 gene on 2B chromosome. It has been suggested that the quantitative trait loci (QTL) mapped to the chromosome 5BL may be new loci inherited from the T. timopheevii. It can be inferred that a number of Russian wheat varieties may contain the Sr17 gene, which does not currently provide effective protection against pathogen. This is the first report describing the results of analysis of the genetic factors conferring resistance of Russian spring wheat varieties to stem rust. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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22 pages, 1131 KiB

Open AccessArticle

Phytoene synthase 1 (Psy-1) and lipoxygenase 1 (Lpx-1) Genes Influence on Semolina Yellowness in Wheat Mediterranean Germplasm

by Roberto Parada, Conxita Royo, Agata Gadaleta, Pasqualina Colasuonno, Ilaria Marcotuli, Iván Matus, Dalma Castillo, Adriano Costa de Camargo, Jorge Araya-Flores, Dolors Villegas and Andrés R. Schwember

Int. J. Mol. Sci. 2020, 21(13), 4669; https://doi.org/10.3390/ijms21134669 - 30 Jun 2020

Cited by 8 | Viewed by 2989

Abstract

Phytoene synthase 1 (Psy1) and lipoxygenase 1 (Lpx-1) are key genes involved in the synthesis and catalysis of carotenoid pigments in durum wheat, regulating the increase and decrease in these compounds, respectively, resulting in the distinct yellow color of [...] Read more.

Phytoene synthase 1 (Psy1) and lipoxygenase 1 (Lpx-1) are key genes involved in the synthesis and catalysis of carotenoid pigments in durum wheat, regulating the increase and decrease in these compounds, respectively, resulting in the distinct yellow color of semolina and pasta. Here, we reported new haplotype variants and/or allele combinations of these two genes significantly affecting yellow pigment content in grain and semolina through their effect on carotenoid pigments. To reach the purpose of this work, three complementary approaches were undertaken: the identification of QTLs associated to carotenoid content on a recombinant inbred line (RIL) population, the characterization of a Mediterranean panel of accessions for Psy1 and Lpx-1 genes, and monitoring the expression of Psy1 and Lpx-1 genes during grain filling on two genotypes with contrasting yellow pigments. Our data suggest that Psy1 plays a major role during grain development, contributing to semolina yellowness, and Lpx-1 appears to be more predominant at post-harvest stages and during pasta making. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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14 pages, 2007 KiB

Open AccessArticle

Septoria Leaf Blotch and Reduced Nitrogen Availability Alter WRKY Transcription Factor Expression in a Codependent Manner

by Alistair A. Poll, Jack Lee, Roy A. Sanderson, Ed Byrne, John A. Gatehouse, Ari Sadanandom, Angharad M. R. Gatehouse and Martin G. Edwards

Int. J. Mol. Sci. 2020, 21(11), 4165; https://doi.org/10.3390/ijms21114165 - 11 Jun 2020

Cited by 4 | Viewed by 2590

Abstract

A major cause of yield loss in wheat worldwide is the fungal pathogen Zymoseptoria tritici, a hemibiotrophic fungus which causes Septoria leaf blotch, the most destructive wheat disease in Europe. Resistance in commercial wheat varieties is poor, however, a link between reduced [...] Read more.

A major cause of yield loss in wheat worldwide is the fungal pathogen Zymoseptoria tritici, a hemibiotrophic fungus which causes Septoria leaf blotch, the most destructive wheat disease in Europe. Resistance in commercial wheat varieties is poor, however, a link between reduced nitrogen availability and increased Septoria tolerance has been observed. We have shown that Septoria load is not affected by nitrogen, whilst the fungus is in its first, symptomless stage of growth. This suggests that a link between nitrogen and Septoria is only present during the necrotrophic phase of Septoria infection. Quantitative real-time PCR data demonstrated that WRKYs, a superfamily of plant-specific transcription factors, are differentially expressed in response to both reduced nitrogen and Septoria. WRKY39 was downregulated over 30-fold in response to necrotrophic stage Septoria, whilst changes in the expression of WRKY68a during the late biotrophic phase were dependent on the concentration of nitrogen under which wheat is grown. WRKY68a may therefore mediate a link between nitrogen and Septoria. The potential remains to identify key regulators in the link between nitrogen and Septoria, and as such, elucidate molecular markers for wheat breeding, or targets for molecular-based breeding approaches. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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13 pages, 1977 KiB

Open AccessArticle

Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat

by Tao Liu, Lijun Wu, Xiaolong Gan, Wenjie Chen, Baolong Liu, George Fedak, Wenguang Cao, Dawn Chi, Dengcai Liu, Huaigang Zhang and Bo Zhang

Int. J. Mol. Sci. 2020, 21(11), 3960; https://doi.org/10.3390/ijms21113960 - 31 May 2020

Cited by 16 | Viewed by 2581

Abstract

Thousand-grain weight (TGW) is a very important yield trait of crops. In the present study, we performed quantitative trait locus (QTL) analysis of TGW in a doubled haploid population obtained from a cross between the bread wheat cultivar “Superb” and the breeding line [...] Read more.

Thousand-grain weight (TGW) is a very important yield trait of crops. In the present study, we performed quantitative trait locus (QTL) analysis of TGW in a doubled haploid population obtained from a cross between the bread wheat cultivar “Superb” and the breeding line “M321” using the wheat 55-k single-nucleotide polymorphism (SNP) genotyping assay. A genetic map containing 15,001 SNP markers spanning 2209.64 cM was constructed, and 9 QTLs were mapped to chromosomes 1A, 2D, 4B, 4D, 5A, 5D, 6A, and 6D based on analyses conducted in six experimental environments during 2015–2017. The effects of the QTLs qTgw.nwipb-4DS and qTgw.nwipb-6AL were shown to be strong and stable in different environments, explaining 15.31–32.43% and 21.34–29.46% of the observed phenotypic variance, and they were mapped within genetic distances of 2.609 cM and 5.256 cM, respectively. These novel QTLs may be used in marker-assisted selection in wheat high-yield breeding. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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18 pages, 4057 KiB

Open AccessArticle

Molecular Markers Associated with Agro-Physiological Traits under Terminal Drought Conditions in Bread Wheat

by Sajid Shokat, Deepmala Sehgal, Prashant Vikram, Fulai Liu and Sukhwinder Singh

Int. J. Mol. Sci. 2020, 21(9), 3156; https://doi.org/10.3390/ijms21093156 - 30 Apr 2020

Cited by 37 | Viewed by 4488

Abstract

Terminal drought stress poses a big challenge to sustain wheat grain production in rain-fed environments. This study aimed to utilize the genetically diverse pre-breeding lines for identification of genomic regions associated with agro-physiological traits at terminal stage drought stress in wheat. A total [...] Read more.

Terminal drought stress poses a big challenge to sustain wheat grain production in rain-fed environments. This study aimed to utilize the genetically diverse pre-breeding lines for identification of genomic regions associated with agro-physiological traits at terminal stage drought stress in wheat. A total of 339 pre-breeding lines panel derived from three-way crosses of ‘exotics × elite × elite’ lines were evaluated in field conditions at Obregon, Mexico for two years under well irrigated as well as drought stress environments. Drought stress was imposed at flowering by skipping the irrigations at pre and post anthesis stage. Results revealed that drought significantly reduced grain yield (Y), spike length (SL), number of grains spikes⁻¹ (NGS) and thousand kernel weight (TKW), while kernel abortion (KA) was increased. Population structure analysis in this panel uncovered three sub-populations. Genome wide linkage disequilibrium (LD) decay was observed at 2.5 centimorgan (cM). The haplotypes-based genome wide association study (GWAS) identified significant associations of Y, SL, and TKW on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12), respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were found for NGS while on chromosome 3A (HB7.12) for KA. The genomic analysis information generated in the study can be efficiently utilized to improve Y and/or related parameters under terminal stage drought stress through marker-assisted breeding. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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15 pages, 3670 KiB

Open AccessArticle

Genome-Scale Analysis of Homologous Genes among Subgenomes of Bread Wheat (Triticum aestivum L.)

by Caie Zhou, Zhaonian Dong, Ting Zhang, Jianhui Wu, Shizhou Yu, Qingdong Zeng, Dejun Han and Wei Tong

Int. J. Mol. Sci. 2020, 21(8), 3015; https://doi.org/10.3390/ijms21083015 - 24 Apr 2020

Cited by 11 | Viewed by 2707

Abstract

Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by [...] Read more.

Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) revealed a total of 88,733 high-confidence homologous genes of four major types (1:1:1, 1:1:0, 0:1:1 and 1:0:1) among the A, B and D subgenomes of wheat. This data was used to compare homologous gene densities among chromosomes, clarify their distribution and correspondence relationship, and compare their functional enrichment. The average density of 1:1:1 homologous genes was about 10 times more than the density of the other three types of homologous genes, although the homologous gene densities of the various chromosomes were similar within each homologous type. Three regions of exceptional density were detected in 1:1:1 homologous genes, the isolate peak on the tail of chromosome 4A, and the desert regions at the start of chromosome 7A and 7D. The correspondence between homologous genes of the wheat subgenomes demonstrated translocation between the tail segments of chromosome 4A and 5A, and the inversion of the segment of original 5A and 7B into the tail of 4A. The homologous genes on the inserting segments of 5A and 7B to 4A were highly enriched in nitrogen, primary metabolite and small molecular metabolism processes, compared with genes on other regions of the original 4A chromosome. This study provides a refined genome-scale reference of homologous genes for wheat molecular research and breeding, which will help to broaden the application of the wheat genome and can be used as a template for research on other polyploid plants. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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25 pages, 3115 KiB

Open AccessArticle

Physiological and Proteomic Dissection of the Responses of Two Contrasting Wheat Genotypes to Nitrogen Deficiency

by Mohammad Rezaul Karim, Ruonan Wang, Lu Zheng, Xiaoying Dong, Renfang Shen and Ping Lan

Int. J. Mol. Sci. 2020, 21(6), 2119; https://doi.org/10.3390/ijms21062119 - 19 Mar 2020

Cited by 10 | Viewed by 2773

Abstract

Nitrogen deficiency usually occurs along with aluminum toxicity in acidic soil, which is one of the major constraints for wheat production worldwide. In order to compare adaptive processes to N deficiency with different Al-tolerant wheat cultivars, we chose Atlas 66 and Scout 66 [...] Read more.

Nitrogen deficiency usually occurs along with aluminum toxicity in acidic soil, which is one of the major constraints for wheat production worldwide. In order to compare adaptive processes to N deficiency with different Al-tolerant wheat cultivars, we chose Atlas 66 and Scout 66 to comprehensively analyze the physiological responses to N deficiency, coupled with label-free mass spectrometry-based proteomics analysis. Results showed that both cultivars were comparable in most physiological indexes under N deficient conditions. However, the chlorophyll content in Scout 66 was higher than that of Atlas 66 under N deficiency. Further proteomic analysis identified 5592 and 5496 proteins in the leaves of Atlas 66 and Scout 66, respectively, of which 658 and 734 proteins were shown to significantly change in abundance upon N deficiency, respectively. The majority of the differentially expressed proteins were involved in cellular N compound metabolic process, photosynthesis, etc. Moreover, tetrapyrrole synthesis and sulfate assimilation were particularly enriched in Scout 66. Our findings provide evidence towards a better understanding of genotype-dependent responses under N deficiency which could help us to develop N efficient cultivars to various soil types. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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Review

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19 pages, 2443 KiB

Open AccessReview

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

by Osvin Arriagada, Ilaria Marcotuli, Agata Gadaleta and Andrés R. Schwember

Int. J. Mol. Sci. 2020, 21(19), 7021; https://doi.org/10.3390/ijms21197021 - 24 Sep 2020

Cited by 17 | Viewed by 3456

Abstract

Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for [...] Read more.

Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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18 pages, 2269 KiB

Open AccessReview

Non-Starch Polysaccharides in Durum Wheat: A Review

by Ilaria Marcotuli, Pasqualina Colasuonno, Yves S. Y. Hsieh, Geoffrey B. Fincher and Agata Gadaleta

Int. J. Mol. Sci. 2020, 21(8), 2933; https://doi.org/10.3390/ijms21082933 - 22 Apr 2020

Cited by 31 | Viewed by 5359

Abstract

Durum wheat is one of most important cereal crops that serves as a staple dietary component for humans and domestic animals. It provides antioxidants, proteins, minerals and dietary fibre, which have beneficial properties for humans, especially as related to the health of gut [...] Read more.

Durum wheat is one of most important cereal crops that serves as a staple dietary component for humans and domestic animals. It provides antioxidants, proteins, minerals and dietary fibre, which have beneficial properties for humans, especially as related to the health of gut microbiota. Dietary fibre is defined as carbohydrate polymers that are non-digestible in the small intestine. However, this dietary component can be digested by microorganisms in the large intestine and imparts physiological benefits at daily intake levels of 30–35 g. Dietary fibre in cereal grains largely comprises cell wall polymers and includes insoluble (cellulose, part of the hemicellulose component and lignin) and soluble (arabinoxylans and (1,3;1,4)-β-glucans) fibre. More specifically, certain components provide immunomodulatory and cholesterol lowering activity, faecal bulking effects, enhanced absorption of certain minerals, prebiotic effects and, through these effects, reduce the risk of type II diabetes, cardiovascular disease and colorectal cancer. Thus, dietary fibre is attracting increasing interest from cereal processors, producers and consumers. Compared with other components of the durum wheat grain, fibre components have not been studied extensively. Here, we have summarised the current status of knowledge on the genetic control of arabinoxylan and (1,3;1,4)-β-glucan synthesis and accumulation in durum wheat grain. Indeed, the recent results obtained in durum wheat open the way for the improvement of these important cereal quality parameters. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping)

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