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Zhang D, Li YY, Zhao X, Zhang C, Liu DK, Lan S, Yin W, Liu ZJ. Molecular insights into self-incompatibility systems: From evolution to breeding. PLANT COMMUNICATIONS 2024; 5:100719. [PMID: 37718509 PMCID: PMC10873884 DOI: 10.1016/j.xplc.2023.100719] [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: 03/29/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Plants have evolved diverse self-incompatibility (SI) systems for outcrossing. Since Darwin's time, considerable progress has been made toward elucidating this unrivaled reproductive innovation. Recent advances in interdisciplinary studies and applications of biotechnology have given rise to major breakthroughs in understanding the molecular pathways that lead to SI, particularly the strikingly different SI mechanisms that operate in Solanaceae, Papaveraceae, Brassicaceae, and Primulaceae. These best-understood SI systems, together with discoveries in other "nonmodel" SI taxa such as Poaceae, suggest a complex evolutionary trajectory of SI, with multiple independent origins and frequent and irreversible losses. Extensive exploration of self-/nonself-discrimination signaling cascades has revealed a comprehensive catalog of male and female identity genes and modifier factors that control SI. These findings also enable the characterization, validation, and manipulation of SI-related factors for crop improvement, helping to address the challenges associated with development of inbred lines. Here, we review current knowledge about the evolution of SI systems, summarize key achievements in the molecular basis of pollen‒pistil interactions, discuss potential prospects for breeding of SI crops, and raise several unresolved questions that require further investigation.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Weilun Yin
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Crain J, Larson S, Dorn K, DeHaan L, Poland J. Genetic architecture and QTL selection response for Kernza perennial grain domestication traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2769-2784. [PMID: 35763029 PMCID: PMC9243872 DOI: 10.1007/s00122-022-04148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication. Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8-5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an FST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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Chapman EA, Thomsen HC, Tulloch S, Correia PMP, Luo G, Najafi J, DeHaan LR, Crews TE, Olsson L, Lundquist PO, Westerbergh A, Pedas PR, Knudsen S, Palmgren M. Perennials as Future Grain Crops: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2022; 13:898769. [PMID: 35968139 PMCID: PMC9372509 DOI: 10.3389/fpls.2022.898769] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.
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Affiliation(s)
| | | | - Sophia Tulloch
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Pedro M. P. Correia
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Javad Najafi
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Lennart Olsson
- Lund University Centre for Sustainability Studies, Lund, Sweden
| | - Per-Olof Lundquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pai Rosager Pedas
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Søren Knudsen
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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Jones TA, Monaco TA, Larson SR, Hamerlynck EP, Crain JL. Using Genomic Selection to Develop Performance-Based Restoration Plant Materials. Int J Mol Sci 2022; 23:ijms23158275. [PMID: 35955409 PMCID: PMC9368130 DOI: 10.3390/ijms23158275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Thomas A. Jones
- USDA-Agricultural Research Service, Forage & Range Research Laboratory, 696 North 1100 East, Logan, UT 84322, USA; (T.A.M.); (S.R.L.)
- Correspondence:
| | - Thomas A. Monaco
- USDA-Agricultural Research Service, Forage & Range Research Laboratory, 696 North 1100 East, Logan, UT 84322, USA; (T.A.M.); (S.R.L.)
| | - Steven R. Larson
- USDA-Agricultural Research Service, Forage & Range Research Laboratory, 696 North 1100 East, Logan, UT 84322, USA; (T.A.M.); (S.R.L.)
| | - Erik P. Hamerlynck
- USDA-Agricultural Research Service, Range & Meadow Forage Management Research Laboratory, 67826-A Highway 205, Burns, OR 97720, USA;
| | - Jared L. Crain
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton PSC, Manhattan, KS 66506, USA;
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Laugerotte J, Baumann U, Sourdille P. Genetic control of compatibility in crosses between wheat and its wild or cultivated relatives. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:812-832. [PMID: 35114064 PMCID: PMC9055826 DOI: 10.1111/pbi.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/26/2021] [Accepted: 01/20/2022] [Indexed: 05/16/2023]
Abstract
In the recent years, the agricultural world has been progressing towards integrated crop protection, in the context of sustainable and reasoned agriculture to improve food security and quality, and to preserve the environment through reduced uses of water, pesticides, fungicides or fertilisers. For this purpose, one possible issue is to cross-elite varieties widely used in fields for crop productions with exotic or wild genetic resources in order to introduce new diversity for genes or alleles of agronomical interest to accelerate the development of new improved cultivars. However, crossing ability (or crossability) often depends on genetic background of the recipient varieties or of the donor, which hampers a larger use of wild resources in breeding programmes of many crops. In this review, we tried to provide a comprehensive summary of genetic factors controlling crossing ability between Triticeae species with a special focus on the crossability between wheat (Triticum aestivum L.) and rye (Secale cereale), which lead to the creation of Triticale (x Triticosecale Wittm.). We also discussed potential applications of newly identified genes or markers associated with crossability for accelerating wheat and Triticale improvement by application of modern genomics technologies in breeding programmes.
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Affiliation(s)
- Julie Laugerotte
- Genetics, Diversity and Ecophysiology of CerealsINRAEUniversité Clermont‐AuvergneClermont‐FerrandFrance
| | - Ute Baumann
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Pierre Sourdille
- Genetics, Diversity and Ecophysiology of CerealsINRAEUniversité Clermont‐AuvergneClermont‐FerrandFrance
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Bajgain P, Brandvain Y, Anderson JA. Influence of Pollen Dispersal and Mating Pattern in Domestication of Intermediate Wheatgrass, a Novel Perennial Food Crop. FRONTIERS IN PLANT SCIENCE 2022; 13:871130. [PMID: 35574146 PMCID: PMC9096613 DOI: 10.3389/fpls.2022.871130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Intermediate wheatgrass (IWG) is a perennial forage grass that is currently being domesticated as a grain crop. It is a primarily wind-pollinated outcrossing species and expresses severe inbreeding depression when self-pollinated. Characterization of pollen dispersal, mating parameters, and change in genetic diversity due to pollen movement is currently lacking in IWG. In this study, we examined pollen dispersal in an IWG selection nursery by evaluating 846 progeny from 15 mother plants and traced their parentage to 374 fathers. A set of 2,500 genomic loci was used to characterize the population. We assigned paternity to 769 (91%) progeny and the average number of fathers per mother plant was 37, from an average of 56 progeny examined per mother. An extensive number (80%) of pollination events occurred within 10 m of the mother plants. Pollination success was not correlated with trait attributes of the paternal genotypes. Mating system analysis confirmed that IWG is highly outcrossing and inbreeding was virtually absent. Neither genetic diversity nor the genome-estimated trait values of progeny were significantly affected by pollinator distance. The distance of pollinator in an IWG breeding nursery therefore was not found to be a major contributor in maintaining genetic diversity. These findings reveal the pollen dispersal model in IWG for the first time and its effect on genetic diversity, which will be valuable in designing future IWG breeding populations. Information generated and discussed in this study could be applied in understanding gene flow and genetic diversity of other open-pollinated species.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, United States
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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Altendorf KR, DeHaan LR, Larson SR, Anderson JA. QTL for seed shattering and threshability in intermediate wheatgrass align closely with well-studied orthologs from wheat, barley, and rice. THE PLANT GENOME 2021; 14:e20145. [PMID: 34626160 DOI: 10.1002/tpg2.20145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Perennial grain crops have the potential to improve agricultural sustainability but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small-grain crops. Marker-aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we use the IWG nested association mapping (NAM) population, with 1,168 F1 progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 single nucleotide polymorphism (SNP) markers and linkage mapping-both within-family and combined across families-with a robust phenotypic dataset collected from four unique year-by-location combinations. A total of 29 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, and most large-effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary depending on the family. In some cases, these QTL align within 216 bp to 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.
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Affiliation(s)
- Kayla R Altendorf
- USDA-ARS Forage Seed and Cereal Research Unit, Prosser, WA, 99350, USA
| | | | - Steve R Larson
- USDA-ARS Forage & Range Research Lab, Logan, UT, 84322, USA
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, 55108, USA
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Miller-Crews I, Matz MV, Hofmann HA. A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples. Forensic Sci Int Genet 2021; 55:102590. [PMID: 34509741 DOI: 10.1016/j.fsigen.2021.102590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 11/24/2022]
Abstract
Next-generation sequencing technology has revolutionized genotyping in many fields of study, yet parentage analysis often still relies on microsatellite markers that are costly to generate and are currently available only for a limited number of species. 2b-RAD sequencing (2b-RAD) is a DNA sequencing technique developed for ecological population genomics that utilizes type IIB restriction enzymes to generate consistent, uniform fragments across samples. This technology is inexpensive, effective with low DNA inputs, and robust to DNA degradation. Here, we developed a probabilistic genotyping-by-sequencing genetic testing pipeline for parentage analysis by using 2b-RAD for inferring familial relationships from mixed DNA samples and populations. Our approach to partial paternity assignment utilizes a novel weighted outlier paternity index (WOPI) adapted for next-generation sequencing data and an identity-by-state (IBS) matrix-based clustering method for pedigree reconstruction. The combination of these two parentage assignment methods overcomes two major obstacles faced by other genetic testing methods: 1) It allows detection of parentage when closely related or inbred individuals are in the alleged parent population (e.g., in laboratory strains); and 2) it resolves mixed DNA samples. We successfully demonstrate this novel approach by correctly inferring paternity for samples pooled from multiple offspring (i.e., entire clutches) in a highly inbred population of an East African cichlid fish. The unique advantages of 2b-RAD in combination with our bioinformatics pipeline enable straightforward and cost-effective parentage analysis in any species regardless of genomic resources available.
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Affiliation(s)
- Isaac Miller-Crews
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Institue for Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA.
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