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Choquette NE, Weldekidan T, Brewer J, Davis SB, Wisser RJ, Holland JB. Enhancing adaptation of tropical maize to temperate environments using genomic selection. G3 (BETHESDA, MD.) 2023; 13:jkad141. [PMID: 37368984 PMCID: PMC10468305 DOI: 10.1093/g3journal/jkad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
Tropical maize can be used to diversify the genetic base of temperate germplasm and help create climate-adapted cultivars. However, tropical maize is unadapted to temperate environments, in which sensitivities to long photoperiods and cooler temperatures result in severely delayed flowering times, developmental defects, and little to no yield. Overcoming this maladaptive syndrome can require a decade of phenotypic selection in a targeted, temperate environment. To accelerate the incorporation of tropical diversity in temperate breeding pools, we tested if an additional generation of genomic selection can be used in an off-season nursery where phenotypic selection is not very effective. Prediction models were trained using flowering time recorded on random individuals in separate lineages of a heterogenous population grown at two northern U.S. latitudes. Direct phenotypic selection and genomic prediction model training was performed within each target environment and lineage, followed by genomic prediction of random intermated progenies in the off-season nursery. Performance of genomic prediction models was evaluated on self-fertilized progenies of prediction candidates grown in both target locations in the following summer season. Prediction abilities ranged from 0.30 to 0.40 among populations and evaluation environments. Prediction models with varying marker effect distributions or spatial field effects had similar accuracies. Our results suggest that genomic selection in a single off-season generation could increase genetic gains for flowering time by more than 50% compared to direct selection in summer seasons only, reducing the time required to change the population mean to an acceptably adapted flowering time by about one-third to one-half.
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Affiliation(s)
- Nicole E Choquette
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Jason Brewer
- USDA-ARS Plant Science Research Unit, Raleigh, NC 27695, USA
| | - Scott B Davis
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Randall J Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L’Institut Agro, Montpellier, FR 34000, USA
| | - James B Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
- USDA-ARS Plant Science Research Unit, Raleigh, NC 27695, USA
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Sorsa Z, Mohammed W, Wegary D, Tarkegne A. Performances of three-way cross hybrids over their respective single crosses and related heterosis of maize ( Zea mays L.) hybrids evaluated in Ethiopia. Heliyon 2023; 9:e15513. [PMID: 37144203 PMCID: PMC10151324 DOI: 10.1016/j.heliyon.2023.e15513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023] Open
Abstract
Less attention had been given to the performances of three-way crosses and its comparative advantages of these hybrids over single crosses. This study was carried out to evaluate the performances of three-way crosses in comparison to single crosses for yield and related agronomic traits and to estimate the magnitude of heterosis. The trial was laid out in a simple alpha lattice design of 10 × 6 for lines, 6 × 5 for single crosses (SC), and 9 × 5 for three way-crosses and planted in adjacent plots in the 2019 cropping season in three locations namely Ambo, Abala-Farcha and Melkassa. Single cross hybrids showed a highly significant (P<1%) variation for grain yield, plant height, ear height, and ear length at three locations. These single cross hybrids had showed also a highly significant genotype by environment interaction (P < 1%) for grain yield, plant height, ear height and kernel per ear. Regarding three-way crosses, there was a significant variation (P<5%) on grain yield in Ambo and Melkassa but on ear height and rows per ear in Abala-Faracho. The genotype × environment interaction was significantly varied for grain yield, ear height and ear length. In the comparison, 80% crosses in Ambo, 73% in Abala-Faracho and 67% in Melkassa showed that three-way crosses were better in their performance than that of their respective single crosses. On the other hand, the single crosses that out-performed their respective three-way crosses were higher in Melkassa than Abala-Faracho and the least were reported from Ambo. Similarly, the maximum better and mid-parent heterosis was from single cross 1(769%) in Ambo and single cross 7 (104%) in Melkassa whereas TWC 14 (52%) and TWC 24 (78%) were the highest better and mid-parent heterosis, respectively in Ambo, TWC1 (56%), and TWC30 (25%) were the highest BPH, and MPH, respectively in Melkassa.
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Affiliation(s)
- Zemach Sorsa
- Department of Plant Science, Wolaita Sodo University, Wolaita Sodo, Ethiopia
- Corresponding author.
| | - Wassu Mohammed
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Dagne Wegary
- International Maize and Wheat Improvement Centre (CIMMYT), Harare, Zimbabwe
| | - Amsal Tarkegne
- Zambia Seed Company Limited, Ingwezi 11066A, Roma, Lusaka, Zambia
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Dermail A, Lübberstedt T, Suwarno WB, Chankaew S, Lertrat K, Ruanjaichon V, Suriharn K. Combining ability of tropical × temperate maize inducers for haploid induction rate, R1-nj seed set, and agronomic traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1154905. [PMID: 37113598 PMCID: PMC10126284 DOI: 10.3389/fpls.2023.1154905] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In vivo maternal haploid induction in isolation fields is proposed to bypass the workload and resource constraints existing in haploid induction nurseries. A better understanding of combining ability and gene action conditioning traits related to hybrid inducers is necessary to set the breeding strategy including to what extent parent-based hybrid prediction is feasible. This study aimed to evaluate the following in tropical savanna in the rainy and dry seasons for haploid induction rate (HIR), R1-nj seed set, and agronomic traits: 1) combining ability, line per se, and hybrid performance of three genetic pools; 2) genetic parameters, the modes of gene action, and heterosis; and 3) the relationships of inbred-general combining ability (GCA) and inbred-hybrid performance. Fifty-six diallel crosses derived from eight maize genotypes were evaluated in the rainy season of 2021 and the dry season of 2021/2022. Reciprocal cross effects including the maternal effect barely contributed to the genotypic variance for each trait observed. HIR, R1-nj seed set, flowering dates, and ear position were highly heritable and additive inherited, while ear length showed dominant inheritance. The equal importance of additive and dominance effects was found for yield-related traits. Temperate inducer BHI306 was the best general combiner for the HIR and R1-nj seed set, followed by two tropical inducers, KHI47 and KHI54. The ranges of heterosis were trait-dependent and slightly influenced by the environment, where hybrids in the rainy season consistently had higher heterosis than those in the dry season for each trait observed. Both hybrid groups derived from tropical × tropical and tropical × temperate inducers showed taller plants, larger ear size, and higher seed sets than the corresponding parents. However, their HIRs were still below the standard check of BHI306. The implications of genetic information, combining ability, and inbred-GCA and inbred-hybrid relationships on breeding strategies are discussed.
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Affiliation(s)
- Abil Dermail
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | | | - Willy Bayuardi Suwarno
- Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia
| | - Sompong Chankaew
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
- Plant Breeding Research Center for Sustainable Agriculture, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Kamol Lertrat
- Plant Breeding Research Center for Sustainable Agriculture, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Vinitchan Ruanjaichon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Khundej Suriharn
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
- Plant Breeding Research Center for Sustainable Agriculture, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
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Zhan W, Guo G, Cui L, Rashid MAR, Jiang L, Sun G, Yang J, Zhang Y. Combined transcriptome and metabolome analysis reveals the effects of light quality on maize hybrids. BMC PLANT BIOLOGY 2023; 23:41. [PMID: 36653749 PMCID: PMC9847186 DOI: 10.1186/s12870-023-04059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F1 hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis. RESULTS In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea mays L.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72-92.50%) and differentially accumulated metabolites (84.74-94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid-flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid-flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM. CONCLUSIONS The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype-environment interactions, and have implications for gene mining of heterotic loci to improve maize production.
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Affiliation(s)
- Weimin Zhan
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guanghui Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Lianhua Cui
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Muhammad Abdul Rehman Rashid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Liangliang Jiang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guanghua Sun
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Yanpei Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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Bhardwaj V, Rawat S, Tiwari J, Sood S, Dua VK, Singh B, Lal M, Mangal V, Govindakrishnan PM. Characterizing the Potato Growing Regions in India Using Meteorological Parameters. Life (Basel) 2022; 12:life12101619. [PMID: 36295054 PMCID: PMC9605082 DOI: 10.3390/life12101619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Currently, the multi-location testing of advanced hybrids in India is carried out at 25 centers under the All India Co-ordinated Research Project on Potato (AICRP-P), which is spread across the country. These centres have been chosen to represent different potato growing regions based on soil and agronomic features. However, the reliable deployment of the newly bred varieties in different regions requires a scientific delineation of potato growing zones with homogenous climates. The present study was undertaken to develop homogenous zones in the Indian sub-continent based on the environmental parameters of the potato growing season. A total of 1253 locations were identified across the country as having a plausible potato growing season of at least 70 days with suitable thermal limits. Six variables including five meteorological parameters including Physiological days (P days), Growing degree days (GDD), Mean daily temperature, Mean night temperature and Mean daily incident solar radiation, together with altitude as the sixth variable, were used for Agglomerative Hierarchical Clustering (AHC) and the Principal Component Analysis by Multidimensional Scaling (MDS) technique to derive identical classes. The thematic map of the classes was overlaid on potato growing districts of India using ArcGIS 9.1 software. The study clearly depicted that the clustering technique can effectively delineate the target population of environments (TPE) for potato genotypes performing well at different testing environments in India. The study also identifies target locations for future focus on breeding strategies, especially the high night temperature class having a large expanse in India. This is also vital in view of the impending climate change situation.
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Affiliation(s)
- Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla 171001, India
- Correspondence:
| | - Shashi Rawat
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | - Jagesh Tiwari
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | - Vijay Kumar Dua
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | - Mehi Lal
- ICAR-Central Potato Research Institute, Modipuram 250110, India
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla 171001, India
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Zafar S, You H, Zhang F, Zhu SB, Chen K, Shen C, Wu H, Zhu F, Zhang C, Xu J. Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid. FRONTIERS IN PLANT SCIENCE 2022; 13:977349. [PMID: 36275576 PMCID: PMC9581170 DOI: 10.3389/fpls.2022.977349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Rice productivity has considerably improved due to the effective employment of heterosis, but the genetic basis of heterosis for grain shape and weight remains uncertain. For studying the genetic dissection of heterosis for grain shape/weight and their relationship with grain yield in rice, quantitative trait locus (QTL) mapping was performed on 1,061 recombinant inbred lines (RILs), which was developed by crossing xian/indica rice Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM). Whereas, BC1F1 (a backcross F1) was developed by crossing RILs with Quan9311A (Q9311A) combined with phenotyping in Hefei (HF) and Nanning (NN) environments. Overall, 114 (main-effect, mQTL) and 359 (epistatic QTL, eQTL) were identified in all populations (RIL, BC1F1, and mid-parent heterosis, HMPs) for 1000-grain weight (TGW), grain yield per plant (GYP) and grain shape traits including grain length (GL), grain width (GW), and grain length to width ratio (GLWR). Differential QTL detection revealed that all additive loci in RILs population do not show heterotic effects, and few of them affect the performance of BC1F1. However, 25 mQTL not only contributed to BC1F1's performance but also contributed to heterosis. A total of seven QTL regions was identified, which simultaneously affected multiple grain traits (grain yield, weight, shape) in the same environment, including five regions with opposite directions and two regions with same directions of favorable allele effects, indicating that partial genetic overlaps are existed between different grain traits. This study suggested different approaches for obtaining good grain quality with high yield by pyramiding or introgressing favorable alleles (FA) with the same direction of gene effect at the QTL regions affecting grain shape/weight and grain yield distributing on different chromosomes, or introgressing or pyramiding FA in the parents instead of fixing additive effects in hybrid as well as pyramiding the polymorphic overdominant/dominant loci between the parents and eliminating underdominant loci from the parents. These outcomes offer valuable information and strategy to develop hybrid rice with suitable grain type and weight.
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Affiliation(s)
- Sundus Zafar
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui You
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuang Bin Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hezhou Wu
- Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China
| | - Fangjin Zhu
- Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China
| | | | - Jianlong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Hainan Yazhou Bay Seed Lab/National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Baldauf JA, Liu M, Vedder L, Yu P, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids. PLANT PHYSIOLOGY 2022; 189:1625-1638. [PMID: 35522211 PMCID: PMC9237695 DOI: 10.1093/plphys/kiac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The dominance model of heterosis explains the superior performance of F1-hybrids via the complementation of deleterious alleles by beneficial alleles in many genes. Genes active in one parent but inactive in the second lead to single-parent expression (SPE) complementation in maize (Zea mays L.) hybrids. In this study, SPE complementation resulted in approximately 700 additionally active genes in different tissues of genetically diverse maize hybrids on average. We established that the number of SPE genes is significantly associated with mid-parent heterosis (MPH) for all surveyed phenotypic traits. In addition, we highlighted that maternally (SPE_B) and paternally (SPE_X) active SPE genes enriched in gene co-expression modules are highly correlated within each SPE type but separated between these two SPE types. While SPE_B-enriched co-expression modules are positively correlated with phenotypic traits, SPE_X-enriched modules displayed a negative correlation. Gene ontology term enrichment analyses indicated that SPE_B patterns are associated with growth and development, whereas SPE_X patterns are enriched in defense and stress response. In summary, these results link the degree of phenotypic MPH to the prevalence of gene expression complementation observed by SPE, supporting the notion that hybrids benefit from SPE complementation via its role in coordinating maize development in fluctuating environments.
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Affiliation(s)
- Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | | | - Lucia Vedder
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Hans-Peter Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany
| | - Heiko Schoof
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210, USA
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Michel KJ, Lima DC, Hundley H, Singan V, Yoshinaga Y, Daum C, Barry K, Broman KW, Buell CR, de Leon N, Kaeppler SM. Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population. Genetics 2022; 221:6571196. [PMID: 35441688 PMCID: PMC9157087 DOI: 10.1093/genetics/iyac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/08/2022] [Indexed: 11/12/2022] Open
Abstract
The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930's. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a six parent multiparent advanced generation intercross (MAGIC) population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in two field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to two testers, respectively, and evaluated as hybrids in two locations in 2018 and 2019 using an incomplete block design. Markers were derived from a Practical Haplotype Graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and two sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55 to 0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49 to 0.55). Overall, this finding is consistent with the overlapping and non-overlapping significant QTL found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.
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Affiliation(s)
- Kathryn J Michel
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dayane C Lima
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hope Hundley
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Vasanth Singan
- Ambry Genetics, 1 Enterprise, Aliso Viejo, CA-92656, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Karl W Broman
- Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WI 53706, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.,Center for Applied Genetic Technologies, Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.,Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Middleton, WI 53562, USA
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9
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Dudits D, Cseri A, Török K, Sass L, Zombori Z, Ferenc G, Poór P, Borbély P, Czékus Z, Vankova R, Dobrev P, Szántó J, Bagi Z, Kovács KL. Triploid Hybrid Vigor in Above-Ground Growth and Methane Fermentation Efficiency of Energy Willow. FRONTIERS IN PLANT SCIENCE 2022; 13:770284. [PMID: 35283877 PMCID: PMC8905242 DOI: 10.3389/fpls.2022.770284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Hybrid vigor and polyploidy are genetic events widely utilized to increase the productivity of crops. Given that bioenergy usage needs to be expanded, we investigated triploid hybrid vigor in terms of the biology of biomass-related willow traits and their relevance to the control of biomethane production. To produce triploid hybrid genotypes, we crossed two female diploid Swedish cultivars (Inger, Tordis) with two male autotetraploid willow (Salix viminalis) variants (PP-E7, PP-E15). Field studies at two locations and in two successive years recorded considerable midparent heterosis (MPH%) in early shoot length that ranged between 11.14 and 68.85% and in the growth rate between 34.12 and 97.18%. The three triploid hybrids (THs) developed larger leaves than their parental cultivars, and the MPH% for their CO2 assimilation rate varied between 0.84 and 25.30%. The impact of hybrid vigor on the concentrations of plant hormones in these TH genotypes reflected essentially different hormonal statuses that depended preferentially on maternal parents. Hybrid vigor was evinced by an elevated concentration of jasmonic acid in shoot meristems of all the three THs (MPH:29.73; 67.08; 91.91%). Heterosis in auxin-type hormones, such as indole-3-acetic acid (MPH:207.49%), phenylacetic acid (MPH:223.51%), and salicylic acid (MPH:27.72%) and benzoic acid (MPH:85.75%), was detectable in the shoots of TH21/2 plants. These hormones also accumulated in their maternal Inger plants. Heterosis in cytokinin-type hormones characterized the shoots of TH3/12 and TH17/17 genotypes having Tordis as their maternal parent. Unexpectedly, we detected abscisic acid as a positive factor in the growth of TH17/17 plants with negative MPH percentages in stomatal conductance and a lower CO2 assimilation rate. During anaerobic digestion, wood raw materials from the triploid willow hybrids that provided positive MPH% in biomethane yield (6.38 and 27.87%) showed negative MPH in their acid detergent lignin contents (from -8.01 to -14.36%). Altogether, these insights into controlling factors of above-ground growth parameters of willow genotypes support the utilization of triploid hybrid vigor in willow breeding to expand the cultivation of short rotation energy trees for renewable energy production.
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Affiliation(s)
- Dénes Dudits
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - András Cseri
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Katalin Török
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - László Sass
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zoltán Zombori
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Péter Poór
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Péter Borbély
- Department of Biological Resources, Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary
| | - Zalán Czékus
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Radomira Vankova
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Petre Dobrev
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | | | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Kornél L. Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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10
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Yan J, Xu Y, Cheng Q, Jiang S, Wang Q, Xiao Y, Ma C, Yan J, Wang X. LightGBM: accelerated genomically designed crop breeding through ensemble learning. Genome Biol 2021; 22:271. [PMID: 34544450 PMCID: PMC8451137 DOI: 10.1186/s13059-021-02492-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines. LightGBM exhibits superior performance in terms of prediction precision, model stability, and computing efficiency through a series of benchmark tests. We also assess the factors that are essential to ensure the best performance of genomic selection prediction by taking complex scenarios in crop hybrid breeding into account. LightGBM has been implemented as a toolbox, CropGBM, encompassing multiple novel functions and analytical modules to facilitate genomically designed breeding in crops.
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Affiliation(s)
- Jun Yan
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Yuetong Xu
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Qian Cheng
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, China
| | - Shuqin Jiang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Qian Wang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chuang Ma
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiangfeng Wang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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11
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Castro NFDC, Jubilato FC, Guerra LHA, Santos FCAD, Taboga SR, Vilamaior PSL. Therapeutic effects of β-caryophyllene on proliferative disorders and inflammation of the gerbil prostate. Prostate 2021; 81:812-824. [PMID: 34125438 DOI: 10.1002/pros.24177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 05/26/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND The prostate is susceptible to changes in androgen levels, which can play an important role in the development of Benign Prostatic Hyperplasia (BPH). Natural compounds have beneficial properties for organisms and can be an important therapeutic strategy in the treatment of diseases. β-Caryophyllene (BCP) is a phytocannabinoid present in several medicinal and food plants species and has shown beneficial effects in different organs. However, little is known about its effects on the prostate. The present study seeks to evaluate the effects of exposure to BCP on the morphophysiology of the ventral prostate of adult gerbils supplemented with testosterone. METHODS Animals were distributed into four groups (n = 8/group): Intact control (C); β-Caryophyllene (BCP): β-Caryophyllene (50 mg/kg/day); Testosterone (T): animals received subcutaneous injections of Testosterone Cypionate (3 mg/Kg), on alternate days, for one month and were euthanized 30 days supplementation ended; Testosterone and β-Caryophyllene (TBCP): animals were exposed to testosterone cypionate (3 mg/Kg) to induce hyperplastic alterations followed by daily BCP (50 mg/kg). Morphological, biometric, immunohistochemical, and serological analyses were performed. RESULTS Proliferative disorders and inflammatory foci were present in the ventral prostate of all experimental groups. An increase in the multiplicity of benign intraepithelial neoplasm and subepithelial inflammatory foci was observed in T group. The incidence of intraluminal inflammatory foci and microinvasive carcinoma was verified only in the T group. Cellular rearrangement and tissue remodeling occurred in the prostate of groups exposed to phytocannabinoids. A reduction was observed in the frequency of PHH3 and Cox2 markers in the prostatic epithelium of TBCP in comparison with T. A decrease in F4/80 and CD163 positive macrophages were also observed in the prostatic stroma of the TBCP group in comparison with T. The results suggest that BCP had favorable effects on BPH, reducing the proliferation and frequency of some inflammatory cells. CONCLUSION BCP impacts the tissue remodeling process in the premalignant prostate environment and that the use of this phytocannabinoid can have a promising effect in the handling of BPH.
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Affiliation(s)
- Nayara Fernanda da Costa Castro
- Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, São Paulo, Brazil
| | - Fernanda Costa Jubilato
- Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, São Paulo, Brazil
| | - Luiz Henrique Alves Guerra
- Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, São Paulo, Brazil
| | | | - Sebastião Roberto Taboga
- Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, São Paulo, Brazil
| | - Patrícia Simone Leite Vilamaior
- Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, São Paulo, Brazil
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12
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Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress. Sci Rep 2021; 11:13489. [PMID: 34188147 PMCID: PMC8241847 DOI: 10.1038/s41598-021-92938-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/17/2021] [Indexed: 01/10/2023] Open
Abstract
The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition.
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13
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Meena RK, Reddy KS, Gautam R, Maddela S, Reddy AR, Gudipalli P. Improved photosynthetic characteristics correlated with enhanced biomass in a heterotic F 1 hybrid of maize (Zea mays L.). PHOTOSYNTHESIS RESEARCH 2021; 147:253-267. [PMID: 33555518 DOI: 10.1007/s11120-021-00822-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a phenomenon wherein F1 hybrid often displays phenotypic superiority and surpasses its parents in terms of growth and agronomic traits. Investigations on the physiological and biochemical properties of the heterotic F1 hybrid are important to uncover the mechanisms underlying heterosis in plants. In the present study, the photosynthetic capacity of a heterotic F1 hybrid of Zea mays L. (DHM 117) that exhibited a higher growth rate and increased biomass was compared with its parental inbreds at vegetative and reproductive stages in the field during 2017 and 2018. The net photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (E) as well as foliar carbohydrates were higher in F1 hybrid than parental inbreds at vegetative and reproductive stages. An increase in total chlorophyll content along with better chlorophyll a fluorescence characteristics including effective quantum yield of photosystem II (ΔF/Fm'), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qp) and decreased non-photochemical quenching (NPQ) was observed in F1 hybrid than the parental inbreds. Further, the expression of potential genes related to C4 photosynthesis was considerably upregulated in F1 hybrid than the parental inbreds during vegetative and reproductive stages. Moreover, the F1 hybrid exhibited distinct heterosis in yield with 63% and 62% increase relative to parental inbreds during 2017 and 2018. We conclude that improved photosynthetic efficiency associated with increased foliar carbohydrates could have contributed to higher growth rate, biomass and yield in the F1 hybrid.
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Affiliation(s)
- Rajesh Kumar Meena
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Kanubothula Sitarami Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Ranjana Gautam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Surender Maddela
- Institute of Biotechnology, Prof. Jayashankar Telangana State Agricultural University, Hyderabad, 500 030, Telangana, India
| | - Attipalli Ramachandra Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Padmaja Gudipalli
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India.
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14
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Onofri A, Terzaroli N, Russi L. Linear models for diallel crosses: a review with R functions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:585-601. [PMID: 33156356 PMCID: PMC7843492 DOI: 10.1007/s00122-020-03716-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/23/2020] [Indexed: 05/02/2023]
Abstract
A new R-software procedure for fixed/random Diallel models was developed. We eased the diallel schemes approach by considering them as specific cases with different parameterisations of a general linear model. Diallel experiments are based on a set of possible crosses between some homozygous (inbred) lines. For these experiments, six main diallel models are available in literature, to quantify genetic effects, such as general combining ability (GCA), specific combining ability (SCA), reciprocal (maternal) effects and heterosis. Those models tend to be presented as separate entities, to be fitted by using specialised software. In this manuscript, we reinforce the idea that diallel models should be better regarded as specific cases (different parameterisations) of a general linear model and might be fitted with general purpose software facilities, as used for all other types of linear models. We start from the estimation of fixed genetical effects within the R environment and try to bridge the gap between diallel models, linear models and ordinary least squares estimation (OLS). First, we review the main diallel models in literature. Second, we build a set of tools to enable geneticists, plant/animal breeders and students to fit diallel models by using the most widely known R functions for OLS fitting, i.e. the 'lm()' function and related methods. Here, we give three examples to show how diallel models can be built by using the typical process of GLMs and fitted, inspected and processed as all other types of linear models in R. Finally, we give a fourth example to show how our tools can be also used to fit random/mixed effect diallel models in the Bayesian framework.
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Affiliation(s)
- Andrea Onofri
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Universita' Degli Studi di Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy
| | - Niccolò Terzaroli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Universita' Degli Studi di Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy.
| | - Luigi Russi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Universita' Degli Studi di Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy
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15
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Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O'Connor C, Vaillancourt B, Lipzen A, Daum C, Barry K, de Leon N, Hirsch CD, Buell CR, Kaeppler SM, Springer NM, Hirsch CN. Single-parent expression drives dynamic gene expression complementation in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:93-107. [PMID: 33098691 DOI: 10.1111/tpj.15042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.
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Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
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16
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Li Z, Zhu A, Song Q, Chen HY, Harmon FG, Chen ZJ. Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis. THE PLANT CELL 2020; 32:3706-3722. [PMID: 33004616 PMCID: PMC7721322 DOI: 10.1105/tpc.20.00320] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 05/04/2023]
Abstract
Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.
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Affiliation(s)
- Zhi Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andan Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Helen Y Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Frank G Harmon
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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17
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Wagner MR, Roberts JH, Balint-Kurti P, Holland JB. Heterosis of leaf and rhizosphere microbiomes in field-grown maize. THE NEW PHYTOLOGIST 2020; 228:1055-1069. [PMID: 32521050 DOI: 10.1111/nph.16730] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/28/2020] [Indexed: 05/21/2023]
Abstract
Macroorganisms' genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. We show that inbred lines and hybrids differ consistently in the composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for nonmicrobial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
| | - Joseph H Roberts
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
| | - James B Holland
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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18
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Li Z, Tirado SB, Kadam DC, Coffey L, Miller ND, Spalding EP, Lorenz AJ, de Leon N, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN. Characterizing introgression-by-environment interactions using maize near isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2761-2773. [PMID: 32572549 DOI: 10.1007/s00122-020-03630-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Significant introgression-by-environment interactions are observed for traits throughout development from small introgressed segments of the genome. Relatively small genomic introgressions containing quantitative trait loci can have significant impacts on the phenotype of an individual plant. However, the magnitude of phenotypic effects for the same introgression can vary quite substantially in different environments due to introgression-by-environment interactions. To study potential patterns of introgression-by-environment interactions, fifteen near-isogenic lines (NILs) with > 90% B73 genetic background and multiple Mo17 introgressions were grown in 16 different environments. These environments included five geographical locations with multiple planting dates and multiple planting densities. The phenotypic impact of the introgressions was evaluated for up to 26 traits that span different growth stages in each environment to assess introgression-by-environment interactions. Results from this study showed that small portions of the genome can drive significant genotype-by-environment interaction across a wide range of vegetative and reproductive traits, and the magnitude of the introgression-by-environment interaction varies across traits. Some introgressed segments were more prone to introgression-by-environment interaction than others when evaluating the interaction on a whole plant basis throughout developmental time, indicating variation in phenotypic plasticity throughout the genome. Understanding the profile of introgression-by-environment interaction in NILs is useful in consideration of how small introgressions of QTL or transgene containing regions might be expected to impact traits in diverse environments.
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Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Sara B Tirado
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Dnyaneshwar C Kadam
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Lisa Coffey
- Department of Agronomy, Iowa State University, 1111 WOI Rd, Ames, IA, 50011, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Aaron J Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, 1111 WOI Rd, Ames, IA, 50011, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA.
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19
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Tirado SB, Hirsch CN, Springer NM. UAV-based imaging platform for monitoring maize growth throughout development. PLANT DIRECT 2020; 4:e00230. [PMID: 32524060 PMCID: PMC7278367 DOI: 10.1002/pld3.230] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 05/06/2023]
Abstract
Plant height (PH) data collected at high temporal resolutions can give insight into how genotype and environmental variation influence plant growth. However, in order to increase the temporal resolution of PH data collection, more robust, rapid, and low-cost methods are needed to evaluate field plots than those currently available. Due to their low cost and high functionality, unmanned aerial vehicles (UAVs) provide an efficient means for collecting height at various stages throughout development. We have developed a procedure for utilizing structure from motion algorithms to collect PH from RGB drone imagery and have used this platform to characterize a yield trial consisting of 24 maize hybrids planted in replicate under two dates and three planting densities. PH data was collected using both weekly UAV flights and manual measurements. The comparisons of UAV-based and manually acquired PH measurements revealed sources of error in measuring PH and were used to develop a robust pipeline for generating UAV-based PH estimates. This pipeline was utilized to document differences in the rate of growth between genotypes and planting dates. Our results also demonstrate that growth rates generated by PH measurements collected at multiple timepoints early in development can be useful in improving predictions of PH at the end of the season. This method provides a low cost, high throughput method for evaluating plant growth in response to environmental stimuli on a plot basis that can be implemented at the scale of a breeding program.
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Affiliation(s)
- Sara B. Tirado
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
| | - Candice N. Hirsch
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Nathan M. Springer
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
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20
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Tirado SB, Hirsch CN, Springer NM. UAV-based imaging platform for monitoring maize growth throughout development. PLANT DIRECT 2020; 4:e00230. [PMID: 32524060 DOI: 10.1101/794057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 05/23/2023]
Abstract
Plant height (PH) data collected at high temporal resolutions can give insight into how genotype and environmental variation influence plant growth. However, in order to increase the temporal resolution of PH data collection, more robust, rapid, and low-cost methods are needed to evaluate field plots than those currently available. Due to their low cost and high functionality, unmanned aerial vehicles (UAVs) provide an efficient means for collecting height at various stages throughout development. We have developed a procedure for utilizing structure from motion algorithms to collect PH from RGB drone imagery and have used this platform to characterize a yield trial consisting of 24 maize hybrids planted in replicate under two dates and three planting densities. PH data was collected using both weekly UAV flights and manual measurements. The comparisons of UAV-based and manually acquired PH measurements revealed sources of error in measuring PH and were used to develop a robust pipeline for generating UAV-based PH estimates. This pipeline was utilized to document differences in the rate of growth between genotypes and planting dates. Our results also demonstrate that growth rates generated by PH measurements collected at multiple timepoints early in development can be useful in improving predictions of PH at the end of the season. This method provides a low cost, high throughput method for evaluating plant growth in response to environmental stimuli on a plot basis that can be implemented at the scale of a breeding program.
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Affiliation(s)
- Sara B Tirado
- Department of Agronomy and Plant Genetics University of Minnesota Saint Paul MN USA
- Department of Plant and Microbial Biology University of Minnesota Saint Paul MN USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics University of Minnesota Saint Paul MN USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology University of Minnesota Saint Paul MN USA
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21
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Gionchetta G, Artigas J, Arias-Real R, Oliva F, Romaní AM. Multi-model assessment of hydrological and environmental impacts on streambed microbes in Mediterranean catchments. Environ Microbiol 2020; 22:2213-2229. [PMID: 32227440 DOI: 10.1111/1462-2920.14990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/29/2022]
Abstract
Microbes inhabiting intermittent streambeds are responsible for controlling and developing many biogeochemical processes essential for the ecosystem functions. Although streambed microbiota is adapted to intermittency the intensification of water scarcity and prolonged dry periods may jeopardise their capacity to cope with hydrological changes. This study aims to evaluate whether, and to what extent, the duration of dry periods affects streambed microbial density, diversity, composition (16S rRNA gene diversity) and functions (extracellular enzyme activities and respiration). Our results highlight the fact that hydrology modulates the community composition and, to some extent, the functions carried out under different environmental conditions. The relative abundance of certain taxa inhabiting the driest intermittent communities differs significantly from those found at sites with continuous flow. Microbial functional metrics revealed a progressive increase in recalcitrant carbon degradation activity at sites with an extended dry phase. In contrast, bacterial density and diversity were mainly influenced by the catchment land use, agriculture enhanced density but reduced diversity, and the presence of riparian vegetation supported greater streambed bacterial diversity. From this perspective, a combination of prolonged dryness with reduced riparian vegetation and increased agricultural land cover could compromise the ecosystem functioning by threaten microbially mediated processes linked to the carbon cycle.
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Affiliation(s)
- Giulia Gionchetta
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain
| | - Joan Artigas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France
| | - Rebeca Arias-Real
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Francesc Oliva
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Anna Maria Romaní
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain
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22
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Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng XW, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:116-128. [PMID: 31736145 DOI: 10.1111/tpj.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F1 hybrids (F1 -specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F1 -specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1 -specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1 -specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1 -specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1 -specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1 -specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.
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Affiliation(s)
- Hong Li
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shuqin Jiang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing, 100048, China
| | - Zechuan Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Vidotti MS, Lyra DH, Morosini JS, Granato ÍSC, Quecine MC, de Azevedo JL, Fritsche-Neto R. Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense. PLoS One 2019; 14:e0222788. [PMID: 31536609 PMCID: PMC6752820 DOI: 10.1371/journal.pone.0222788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/07/2019] [Indexed: 11/18/2022] Open
Abstract
Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.
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Affiliation(s)
- Miriam Suzane Vidotti
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (MSV); (RFN)
| | | | - Júlia Silva Morosini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - João Lúcio de Azevedo
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Roberto Fritsche-Neto
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (MSV); (RFN)
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Li Z, Coffey L, Garfin J, Miller ND, White MR, Spalding EP, Leon ND, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN. Correction: Genotype-by-environment interactions affecting heterosis in maize. PLoS One 2019; 14:e0219528. [PMID: 31381609 PMCID: PMC6681948 DOI: 10.1371/journal.pone.0219528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Vidotti MS, Matias FI, Alves FC, Pérez-Rodríguez P, Beltran GA, Burgueño J, Crossa J, Fritsche-Neto R. Maize responsiveness to Azospirillum brasilense: Insights into genetic control, heterosis and genomic prediction. PLoS One 2019; 14:e0217571. [PMID: 31173600 PMCID: PMC6555527 DOI: 10.1371/journal.pone.0217571] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
Several studies have shown differences in the abilities of maize genotypes to facilitate or impede Azospirillum brasilense colonization and to receive benefits from this association. Hence, our aim was to study the genetic control, heterosis effect and the prediction accuracy of the shoot and root traits of maize in response to A. brasilense. For that, we evaluated 118 hybrids under two contrasting scenarios: i) N stress (control) and ii) N stress plus A. brasilense inoculation. The diallel analyses were performed using mixed model equations, and the genomic prediction models accounted for the general and specific combining ability (GCA and SCA, respectively) and the presence or not of G×E effects. In addition, the genomic models were fitted considering parametric (G-BLUP) and semi-parametric (RKHS) kernels. The genotypes showed significant inoculation effect for five root traits, and the GCA and SCA were significant for both. The GCA in the inoculated treatment presented a greater magnitude than the control, whereas the opposite was observed for SCA. Heterosis was weakly influenced by the inoculation, and the heterozygosity and N status in the plant can have a role in the benefits that can be obtained from this Plant Growth-Promoting Bacteria (PGPB). Prediction accuracies for N stress plus A. brasilense ranged from 0.42 to 0.78, depending on the scenario and trait, and were higher, in most cases, than the non-inoculated treatment. Finally, our findings provide an understanding of the quantitative variation of maize responsiveness to A. brasilense and important insights to be applied in maize breeding aiming the development of superior hybrids for this association.
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Affiliation(s)
- Miriam Suzane Vidotti
- Genetics Department, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Filipe Inácio Matias
- Genetics Department, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Filipe Couto Alves
- Department of Epidemiology & Biostatistics, Michigan State University, East Lansing, Michigan, United States of America
| | | | - Gregório Alvarado Beltran
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado de Mexico, Mexico
| | - Juan Burgueño
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado de Mexico, Mexico
| | - José Crossa
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado de Mexico, Mexico
| | - Roberto Fritsche-Neto
- Genetics Department, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Wallace JG, Rodgers-Melnick E, Buckler ES. On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics. Annu Rev Genet 2018; 52:421-444. [DOI: 10.1146/annurev-genet-120116-024846] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.
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Affiliation(s)
- Jason G. Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602, USA
| | | | - Edward S. Buckler
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
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