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Ye J, Yu Z, Wang Y, Lu D, Zhou H. WheatLFANet: in-field detection and counting of wheat heads with high-real-time global regression network. PLANT METHODS 2023; 19:103. [PMID: 37794515 PMCID: PMC10548667 DOI: 10.1186/s13007-023-01079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Detection and counting of wheat heads are of crucial importance in the field of plant science, as they can be used for crop field management, yield prediction, and phenotype analysis. With the widespread application of computer vision technology in plant science, monitoring of automated high-throughput plant phenotyping platforms has become possible. Currently, many innovative methods and new technologies have been proposed that have made significant progress in the accuracy and robustness of wheat head recognition. Nevertheless, these methods are often built on high-performance computing devices and lack practicality. In resource-limited situations, these methods may not be effectively applied and deployed, thereby failing to meet the needs of practical applications. RESULTS In our recent research on maize tassels, we proposed TasselLFANet, the most advanced neural network for detecting and counting maize tassels. Building on this work, we have now developed a high-real-time lightweight neural network called WheatLFANet for wheat head detection. WheatLFANet features a more compact encoder-decoder structure and an effective multi-dimensional information mapping fusion strategy, allowing it to run efficiently on low-end devices while maintaining high accuracy and practicality. According to the evaluation report on the global wheat head detection dataset, WheatLFANet outperforms other state-of-the-art methods with an average precision AP of 0.900 and an R2 value of 0.949 between predicted values and ground truth values. Moreover, it runs significantly faster than all other methods by an order of magnitude (TasselLFANet: FPS: 61). CONCLUSIONS Extensive experiments have shown that WheatLFANet exhibits better generalization ability than other state-of-the-art methods, and achieved a speed increase of an order of magnitude while maintaining accuracy. The success of this study demonstrates the feasibility of achieving real-time, lightweight detection of wheat heads on low-end devices, and also indicates the usefulness of simple yet powerful neural network designs.
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Affiliation(s)
- Jianxiong Ye
- College of Robotics, Guangdong Polytechnic of Science and Technology, Zhuhai, Guangdong, China
| | - Zhenghong Yu
- College of Robotics, Guangdong Polytechnic of Science and Technology, Zhuhai, Guangdong, China.
| | - Yangxu Wang
- College of Robotics, Guangdong Polytechnic of Science and Technology, Zhuhai, Guangdong, China
| | - Dunlu Lu
- College of Robotics, Guangdong Polytechnic of Science and Technology, Zhuhai, Guangdong, China
| | - Huabing Zhou
- Hubei Key Laboratory of Intelligent Robot, Wuhan Institute of Technology, Wuhan, China
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Singh J, Chhabra B, Raza A, Yang SH, Sandhu KS. Important wheat diseases in the US and their management in the 21st century. FRONTIERS IN PLANT SCIENCE 2023; 13:1010191. [PMID: 36714765 PMCID: PMC9877539 DOI: 10.3389/fpls.2022.1010191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/28/2022] [Indexed: 05/27/2023]
Abstract
Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.
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Affiliation(s)
- Jagdeep Singh
- Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Bhavit Chhabra
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Ali Raza
- College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Seung Hwan Yang
- Department of Integrative Biotechnology, Chonnam National University, Yeosu, Republic of Korea
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3
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Sasaki K, Imai R. Mechanisms of cold-induced immunity in plants. PHYSIOLOGIA PLANTARUM 2023; 175:e13846. [PMID: 36546699 DOI: 10.1111/ppl.13846] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Overwintering plants acquire substantial levels of freezing tolerance through cold acclimation or winter hardening. This process is essential for the plants survival to harsh winter conditions. In the areas where persistent snow cover lasts several months, plants are protected from freezing but are, however, exposed to other harsh conditions, such as dark, cold, and high humidity. These conditions facilitate the infection of psychrophilic pathogens, which are termed "snow molds." To fight against infection of snow molds, overwintering plants develop disease resistance via the process of cold acclimation. Compared with pathogen-induced disease resistance, the molecular mechanisms of cold-induced disease resistance have yet to be fully elucidated. In this review, we outline the recent progress in our understanding of disease resistance acquired through cold acclimation.
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Affiliation(s)
- Kentaro Sasaki
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Ryozo Imai
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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Mizuno N, Matsunaka H, Yanaka M, Nakata M, Nakamura K, Nakamaru A, Kiribuchi-Otobe C, Ishikawa G, Chono M, Hatta K, Fujita M, Kobayashi F. Allelic variations of Vrn-1 and Ppd-1 genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time. BREEDING SCIENCE 2022; 72:343-354. [PMID: 36776445 PMCID: PMC9895800 DOI: 10.1270/jsbbs.22017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 05/31/2023]
Abstract
The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Masaru Nakata
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Akiko Nakamaru
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, 4 Akahira, Shimo-kuriyagawa, Morioka, Iwate 020-0198, Japan
| | - Chikako Kiribuchi-Otobe
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Makiko Chono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Koichi Hatta
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Ponomareva M, Gorshkov V, Ponomarev S, Mannapova G, Askhadullin D, Askhadullin D, Gogoleva O, Meshcherov A, Korzun V. Resistance to Snow Mold as a Target Trait for Rye Breeding. PLANTS 2022; 11:plants11192516. [PMID: 36235382 PMCID: PMC9571149 DOI: 10.3390/plants11192516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/26/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022]
Abstract
Winter rye is a versatile crop widely used for food and industry. Although rye is resistant to abiotic stressors and many phytopathogens, it is severely damaged by pink snow mold (SM)—a progressive disease caused by the psychrotolerant fungus Microdochium nivale under the snow cover or during prolonged periods of wet and cool conditions. Due to little use of the SM resistance sources in contemporary breeding, varieties with at least moderate resistance to SM are limited. Our study aimed to integrate field assessment under natural conditions and an artificially enriched infection background with laboratory techniques for testing rye accessions and selecting SM resistant sources for applied breeding programs and genetic research. We revealed valuable sources of SM resistance and split rye accessions, according to the level of the genetic divergence of the SM resistance phenotype. This allowed us to select the most distinct donors of the SM resistance, for their use as parental forms, to include novel variability sources in the breeding program for achieving high genetic variability, as well as enhanced and durable SM resistance, in progeny. The rye accessions analyzed here, and the suggested options for their use in breeding, are valuable tools for rye breeding.
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Affiliation(s)
- Mira Ponomareva
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
- Correspondence: (M.P.); (V.K.)
| | - Vladimir Gorshkov
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Sergey Ponomarev
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Gulnaz Mannapova
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Danil Askhadullin
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Damir Askhadullin
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Olga Gogoleva
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Azat Meshcherov
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Viktor Korzun
- Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
- Correspondence: (M.P.); (V.K.)
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6
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Sandhu KS, Merrick LF, Sankaran S, Zhang Z, Carter AH. Prospectus of Genomic Selection and Phenomics in Cereal, Legume and Oilseed Breeding Programs. Front Genet 2022. [PMCID: PMC8814369 DOI: 10.3389/fgene.2021.829131] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The last decade witnessed an unprecedented increase in the adoption of genomic selection (GS) and phenomics tools in plant breeding programs, especially in major cereal crops. GS has demonstrated the potential for selecting superior genotypes with high precision and accelerating the breeding cycle. Phenomics is a rapidly advancing domain to alleviate phenotyping bottlenecks and explores new large-scale phenotyping and data acquisition methods. In this review, we discuss the lesson learned from GS and phenomics in six self-pollinated crops, primarily focusing on rice, wheat, soybean, common bean, chickpea, and groundnut, and their implementation schemes are discussed after assessing their impact in the breeding programs. Here, the status of the adoption of genomics and phenomics is provided for those crops, with a complete GS overview. GS’s progress until 2020 is discussed in detail, and relevant information and links to the source codes are provided for implementing this technology into plant breeding programs, with most of the examples from wheat breeding programs. Detailed information about various phenotyping tools is provided to strengthen the field of phenomics for a plant breeder in the coming years. Finally, we highlight the benefits of merging genomic selection, phenomics, and machine and deep learning that have resulted in extraordinary results during recent years in wheat, rice, and soybean. Hence, there is a potential for adopting these technologies into crops like the common bean, chickpea, and groundnut. The adoption of phenomics and GS into different breeding programs will accelerate genetic gain that would create an impact on food security, realizing the need to feed an ever-growing population.
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Affiliation(s)
- Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- *Correspondence: Karansher S. Sandhu,
| | - Lance F. Merrick
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Sindhuja Sankaran
- Department of Biological System Engineering, Washington State University, Pullman, WA, United States
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Arron H. Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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7
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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8
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Lozada DN, Nunez G, Lujan P, Dura S, Coon D, Barchenger DW, Sanogo S, Bosland PW. Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2021; 21:601. [PMID: 34922461 PMCID: PMC8684135 DOI: 10.1186/s12870-021-03387-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/07/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. RESULTS Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. CONCLUSIONS Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.
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Affiliation(s)
- Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Guillermo Nunez
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Phillip Lujan
- Extension Plant Sciences, Plant Diagnostic Clinic, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Srijana Dura
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Danise Coon
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Paul W Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA
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9
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Mistletoes and their eucalypt hosts differ in the response of leaf functional traits to climatic moisture supply. Oecologia 2021; 195:759-771. [PMID: 33595714 DOI: 10.1007/s00442-021-04867-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/03/2021] [Indexed: 12/31/2022]
Abstract
Trade-offs between photosynthesis and the costs of resource capture inform economic strategies of plants across environmental gradients and result in predictable variation in leaf traits. However, understudied functional groups like hemiparasites that involve dramatically different strategies for resource capture may have traits that deviate from expectations. We measured leaf traits related to gas exchange in mistletoes and their eucalypt hosts along a climatic gradient in relative moisture supply, measured as the ratio of precipitation to pan evaporation (P/Ep), in Victoria, Australia. We compared traits for mistletoes vs. hosts as functions of relative moisture supply and examined trait-trait correlations in both groups. Eucalypt leaf traits responded strongly to decreasing P/Ep, consistent with economic theory. Leaf area and specific leaf area (SLA) decreased along the P/Ep gradient, while C:N ratio, leaf thickness, N per area, and δ13C all increased. Mistletoes responded overall less strongly to P/Ep based on multivariate analyses; individual traits sometimes shifted in parallel with those of hosts, but SLA, leaf thickness, and N per area showed no significant change across the gradient. For mistletoes, leaf thickness was inversely related to leaf dry matter content (LDMC), with no relationship between SLA and mass-based N. In mistletoes, reduced costs of transpiration (reflecting their lack of roots) and abundant succulent leaf tissue help account for observed differences from their eucalypt hosts. Trait-based analysis of atypical functional types such as mistletoes help refine hypotheses based on plant economics and specialized adaptations to resource limitation.
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10
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Ponomareva ML, Gorshkov VY, Ponomarev SN, Korzun V, Miedaner T. Snow mold of winter cereals: a complex disease and a challenge for resistance breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:419-433. [PMID: 33221940 PMCID: PMC7843483 DOI: 10.1007/s00122-020-03725-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/04/2020] [Indexed: 05/28/2023]
Abstract
Snow mold resistance is a complex quantitative trait highly affected by environmental conditions during winter that must be addressed by resistance breeding. Snow mold resistance in winter cereals is an important trait for many countries in the Northern Hemisphere. The disease is caused by at least four complexes of soilborne fungi and oomycetes of which Microdochium nivale and M. majus are among the most common pathogens. They have a broad host range covering all winter and spring cereals and can basically affect all plant growth stages and organs. Their attack leads to a low germination rate, and/or pre- and post-emergence death of seedlings after winter and, depending on largely unknown environmental conditions, also to foot rot, leaf blight, and head blight. Resistance in winter wheat and triticale is governed by a multitude of quantitative trait loci (QTL) with mainly additive effects highly affected by genotype × environment interaction. Snow mold resistance interacts with winter hardiness in a complex way leading to a co-localization of resistance QTLs with QTLs/genes for freezing tolerance. In practical breeding, a multistep procedure is necessary with (1) freezing tolerance tests, (2) climate chamber tests for snow mold resistance, and (3) field tests in locations with and without regularly occurring snow cover. In the future, resistance sources should be genetically characterized also in rye by QTL mapping or genome-wide association studies. The development of genomic selection procedures should be prioritized in breeding research.
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Affiliation(s)
- Mira L Ponomareva
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, Ul. Lobachevskogo 2/31, Kazan, 420111, Tatarstan, Russian Federation
| | - Vladimir Yu Gorshkov
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, Ul. Lobachevskogo 2/31, Kazan, 420111, Tatarstan, Russian Federation
| | - Sergey N Ponomarev
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, Ul. Lobachevskogo 2/31, Kazan, 420111, Tatarstan, Russian Federation
| | - Viktor Korzun
- Laboratory of Plant Infectious Diseases, FRC Kazan Scientific Center of RAS, Ul. Lobachevskogo 2/31, Kazan, 420111, Tatarstan, Russian Federation
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555, Einbeck, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany.
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11
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Merrick LF, Burke AB, Zhang Z, Carter AH. Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program. FRONTIERS IN PLANT SCIENCE 2021; 12:772907. [PMID: 35154175 PMCID: PMC8831792 DOI: 10.3389/fpls.2021.772907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/29/2021] [Indexed: 05/06/2023]
Abstract
Unknown genetic architecture makes it difficult to characterize the genetic basis of traits and associated molecular markers because of the complexity of small effect quantitative trait loci (QTLs), environmental effects, and difficulty in phenotyping. Seedling emergence of wheat (Triticum aestivum L.) from deep planting, has a poorly understood genetic architecture, is a vital factor affecting stand establishment and grain yield, and is historically correlated with coleoptile length. This study aimed to dissect the genetic architecture of seedling emergence while accounting for correlated traits using one multi-trait genome-wide association study (MT-GWAS) model and three single-trait GWAS (ST-GWAS) models. The ST-GWAS models included one single-locus model [mixed-linear model (MLM)] and two multi-locus models [fixed and random model circulating probability unification (FarmCPU) and Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK)]. We conducted GWAS using two populations. The first population consisted of 473 varieties from a diverse association mapping panel phenotyped from 2015 to 2019. The second population consisted of 279 breeding lines phenotyped in 2015 in Lind, WA, with 40,368 markers. We also compared the inclusion of coleoptile length and markers associated with reduced height as covariates in our ST-GWAS models. ST-GWAS found 107 significant markers across 19 chromosomes, while MT-GWAS found 82 significant markers across 14 chromosomes. The FarmCPU and BLINK models, including covariates, were able to identify many small effect markers while identifying large effect markers on chromosome 5A. By using multi-locus model breeding, programs can uncover the complex nature of traits to help identify candidate genes and the underlying architecture of a trait, such as seedling emergence.
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Genomic Selection in Winter Wheat Breeding Using a Recommender Approach. Genes (Basel) 2020; 11:genes11070779. [PMID: 32664601 PMCID: PMC7397162 DOI: 10.3390/genes11070779] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 12/04/2022] Open
Abstract
Achieving optimal predictive ability is key to increasing the relevance of implementing genomic selection (GS) approaches in plant breeding programs. The potential of an item-based collaborative filtering (IBCF) recommender system in the context of multi-trait, multi-environment GS has been explored. Different GS scenarios for IBCF were evaluated for a diverse population of winter wheat lines adapted to the Pacific Northwest region of the US. Predictions across years through cross-validations resulted in improved predictive ability when there is a high correlation between environments. Using multiple spectral traits collected from high-throughput phenotyping resulted in better GS accuracies for grain yield (GY) compared to using only single traits for predictions. Trait adjustments through various Bayesian regression models using genomic information from SNP markers was the most effective in achieving improved accuracies for GY, heading date, and plant height among the GS scenarios evaluated. Bayesian LASSO had the highest predictive ability compared to other models for phenotypic trait adjustments. IBCF gave competitive accuracies compared to a genomic best linear unbiased predictor (GBLUP) model for predicting different traits. Overall, an IBCF approach could be used as an alternative to traditional prediction models for important target traits in wheat breeding programs.
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Lozada DN, Ward BP, Carter AH. Gains through selection for grain yield in a winter wheat breeding program. PLoS One 2020; 15:e0221603. [PMID: 32343696 PMCID: PMC7188280 DOI: 10.1371/journal.pone.0221603] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022] Open
Abstract
Increased genetic gain for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selection R values across several selection approaches including phenotypic (PS), marker-based (MS), genomic (GS), and a combination of PS and GS (PS+GS). Ten populations of Washington State University (WSU) winter wheat breeding lines including a diversity panel and F5 and double haploid lines evaluated from 2015 to 2019 growing seasons for grain yield in Lind and Pullman, WA, USA were used in the study. Selection was conducted by selecting the top 20% of lines based on observed yield (PS strategy), genomic estimated breeding values (GS), presence of yield "enhancing" alleles of the most significant single nucleotide polymorphism (SNP) markers identified from genome-wide association mapping (MS), and high observed yield and estimated breeding values (PS+GS). Overall, PS compared to other individual selection strategies (MS and GS) showed the highest mean response (R = 0.61) within the same environment. When combined with GS, a 23% improvement in R for yield was observed, indicating that gains could be improved by complementing traditional PS with GS within the same environment. Validating selection strategies in different environments resulted in low to negative R values indicating the effects of genotype-by-environment interactions for grain yield. MS was not successful in terms of R relative to the other selection approaches; using this strategy resulted in a significant (P < 0.05) decrease in response to selection compared with the other approaches. An integrated PS+GS approach could result in optimal genetic gain within the same environment, whereas a PS strategy might be a viable option for grain yield validated in different environments. Altogether, we demonstrated that gains through increased response to selection for yield could be achieved in the WSU winter wheat breeding program by implementing different selection strategies either exclusively or in combination.
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Affiliation(s)
- Dennis N. Lozada
- Crop and Soil Sciences Department, Washington State University, Pullman, WA, United States of America
| | - Brian P. Ward
- USDA-ARS Plant Science Research Unit, Raleigh, NC, United States of America
| | - Arron H. Carter
- Crop and Soil Sciences Department, Washington State University, Pullman, WA, United States of America
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