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Gong W, Proud C, Vinarao R, Fukai S, Mitchell J. Genome-Wide Association Study of Early Vigour-Related Traits for a Rice ( Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions. BIOLOGY 2024; 13:261. [PMID: 38666873 PMCID: PMC11048181 DOI: 10.3390/biology13040261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.
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Affiliation(s)
- Wenliu Gong
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia (J.M.)
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Piarulli L, Pirolo C, Roseti V, Bellin D, Mascio I, La Notte P, Montemurro C, Miazzi MM. Breeding new seedless table grapevines for a more sustainable viticulture in Mediterranean climate. FRONTIERS IN PLANT SCIENCE 2024; 15:1379642. [PMID: 38645394 PMCID: PMC11027070 DOI: 10.3389/fpls.2024.1379642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/14/2024] [Indexed: 04/23/2024]
Abstract
The growing demand for sustainable and environmentally friendly viticulture is leading to a multiplication of breeding programs aimed at obtaining vines that are resistant to powdery mildew (PM) and downy mildew (DM), the two most damaging vine diseases. In Puglia, the most important Italian region for the production of table grapes, an extensive crossing program was launched in 2015 with 113 crosses, including elite table varieties, seedless varieties, and resistant varieties. The main seedling production parameters were measured for each cross. In particular, berries harvested as well as the number of seeds and seedlings obtained were considered. Approximately 103,119 seedlings were obtained and subjected to marker-assisted selection for seedlessness using the marker VvAGL11 and for resistance to PM and DM with appropriate markers. Approximately one third (32,638) of the progenies were selected as putative seedless and seventeen thousand five hundred-nine (17,509) were transferred to the field for phenotypic evaluation, including 527 seedless individuals putatively resistant, of which 208 confirmed to be resistant to DM, 22 resistant to PM, and 20 individuals that combined resistance and seedlessness traits. The work discusses the effects of parental combinations and other variables in obtaining surviving progeny and pyramiding genes in table grapes and provides useful information for selecting genotypes and increasing the efficiency of breeding programs for seedless disease-resistant grapes.
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Affiliation(s)
- Luciana Piarulli
- SINAGRI S.r.l. – Spin-Off of the University of Bari Aldo Moro, Bari, Italy
- Rete Italian Variety Club (IVC), Locorotondo, Italy
| | - Costantino Pirolo
- SINAGRI S.r.l. – Spin-Off of the University of Bari Aldo Moro, Bari, Italy
- Rete Italian Variety Club (IVC), Locorotondo, Italy
| | | | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | - Cinzia Montemurro
- SINAGRI S.r.l. – Spin-Off of the University of Bari Aldo Moro, Bari, Italy
- Rete Italian Variety Club (IVC), Locorotondo, Italy
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Monica Marilena Miazzi
- Rete Italian Variety Club (IVC), Locorotondo, Italy
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
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Garin V, Diallo C, Tékété ML, Théra K, Guitton B, Dagno K, Diallo AG, Kouressy M, Leiser W, Rattunde F, Sissoko I, Touré A, Nébié B, Samaké M, Kholovà J, Berger A, Frouin J, Pot D, Vaksmann M, Weltzien E, Témé N, Rami JF. Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping. Genetics 2024; 226:iyae003. [PMID: 38381593 PMCID: PMC10990433 DOI: 10.1093/genetics/iyae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 02/23/2024] Open
Abstract
Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.
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Affiliation(s)
- Vincent Garin
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Chiaka Diallo
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Département d’Enseignement et de Recherche des Sciences et Techniques Agricoles, Institut polytechnique rural de formation et de recherche appliquée de Katibougou, Koulikoro, BP 06, Mali
| | - Mohamed Lamine Tékété
- Institut d’Economie Rurale, Bamako, BP 262, Mali
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | | | - Baptiste Guitton
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Karim Dagno
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | | | | | - Willmar Leiser
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Fred Rattunde
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Ibrahima Sissoko
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Aboubacar Touré
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Baloua Nébié
- Dryland Crops Program, International Maize and Wheat Improvement Center (CIMMYT-Senegal) U/C CERAAS, Thiès, Po Box 3320, Senegal
| | - Moussa Samaké
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | - Jana Kholovà
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences, Prague, 165 00, Czech Republic
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Julien Frouin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Michel Vaksmann
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Eva Weltzien
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Niaba Témé
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | - Jean-François Rami
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
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Ganaparthi VR, Wechter P, Levi A, Branham SE. Mapping and validation of Fusarium wilt race 2 resistance QTL from Citrullus amarus line USVL246-FR2. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:91. [PMID: 38555543 PMCID: PMC10982098 DOI: 10.1007/s00122-024-04595-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024]
Abstract
KEY MESSAGE Fon race 2 resistant QTLs were identified on chromosomes 8 and 9. Families homozygous for resistance alleles at a haplotype of three KASP markers had 42% lower disease severity than those with susceptible alleles in an independent, interspecific validation population confirming their utility for introgression of Fusarium wilt resistance. Fusarium oxysporum f. sp. niveum (Fon) race 2 causes Fusarium wilt in watermelon and threatens watermelon production worldwide. Chemical management options are not effective, and no resistant edible watermelon cultivars have been released. Implementation of marker-assisted selection to develop resistant cultivars requires identifying sources of resistance and the underlying quantitative trait loci (QTL), developing molecular markers associated with the QTL, and validating marker-phenotype associations with an independent population. An intraspecific Citrullus amarus recombinant inbred line population from a cross of resistant USVL246-FR2 and susceptible USVL114 was used for mapping Fon race 2 resistance QTL. KASP markers were developed (N = 51) for the major QTL on chromosome 9 and minor QTL on chromosomes 1, 6, and 8. An interspecific F2:3 population was developed from resistance donor USVL246-FR2 (C. amarus) and a susceptible cultivar 'Sugar Baby' (Citrullus lanatus) to validate the utility of the markers for introgression of resistance from the wild crop relative into cultivated watermelon. Only 16 KASP markers segregated in the interspecific C. amarus/lanatus validation population. Four markers showed significant differences in the separation of genotypes based on family-mean disease severity, but together explained only 16% of the phenotypic variance. Genotypes that inherited homozygous resistant parental alleles at three KASP markers had 42% lower family-mean disease severity than homozygous susceptible genotypes. Thus, haplotype analysis was more effective at predicting the mean disease severity of families than single markers. The haplotype identified in this study will be valuable for developing Fon race 2 resistant watermelon cultivars.
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Affiliation(s)
| | - Patrick Wechter
- Coastal Research and Education Center, Clemson University, Charleston, SC, USA
| | - Amnon Levi
- USDA, US Vegetable Laboratory, ARS, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Sandra E Branham
- Coastal Research and Education Center, Clemson University, Charleston, SC, USA.
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Wang X, Zhou Y, You C, Yang J, Chen Z, Tang D, Ni J, Li P, Wang L, Zhu K, Deng W, Wu H, Bao R, Liu Z, Meng P, Yang S, Rong T, Liu J. Fine mapping and candidate gene analysis of qSRC3 controlling the silk color in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:90. [PMID: 38555318 DOI: 10.1007/s00122-024-04598-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/09/2024] [Indexed: 04/02/2024]
Abstract
KEY MESSAGE Fine mapping of the maize QTL qSRC3, responsible for red silk, uncovered the candidate gene ZmMYB20, which encodes an R2R3-MYB transcription factor, has light-sensitive expression, and putatively regulates genes expression associated with anthocyanin biosynthesis. Colorless silk is a key characteristic contributing to the visual quality of fresh corn intended for market distribution. Nonetheless, the identification of Mendelian trait loci and associated genes that control silk color has been scarce. In this study, a F2 population arising from the hybridization of the single-segment substitution line qSRC3MT1 with red silk, carrying an introgressed allele from teosinte (Zea mays ssp. mexicana), and the recurrent maize inbred line Mo17, characterized by light green silk, was utilized for fine mapping. We found that the red silk trait is controlled by a semi-dominant genetic locus known as qSRC3, and its expression is susceptible to light-mediated inhibition. Moreover, qSRC3 explained 68.78% of the phenotypic variance and was delimited to a 133.2 kb region, which includes three genes. Subsequent expression analyses revealed that ZmMYB20 (Zm00001d039700), which encodes an R2R3-MYB transcription factor, was the key candidate gene within qSRC3. Yeast one-hybrid and dual-luciferase reporter assays provided evidence that ZmMYB20 suppresses the expression of two crucial anthocyanin biosynthesis genes, namely ZmF3H and ZmUFGT, by directly binding to their respective promoter regions. Our findings underscore the significance of light-inhibited ZmMYB20 in orchestrating the spatial and temporal regulation of anthocyanin biosynthesis. These results advance the production of colorless silk in fresh corn, responding to the misconception that fresh corn with withered colored silk is not fresh and providing valuable genetic resources for the improvement of sweet and waxy maize.
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Affiliation(s)
- Xueying Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chong You
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinchang Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhengjie Chen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dengguo Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jixing Ni
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Le Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kaili Zhu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wujiao Deng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haimei Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ruifan Bao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiqin Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengxu Meng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Sijia Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Naqvi RZ, Mahmood MA, Mansoor S, Amin I, Asif M. Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops. FRONTIERS IN PLANT SCIENCE 2024; 14:1273859. [PMID: 38259913 PMCID: PMC10800452 DOI: 10.3389/fpls.2023.1273859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
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Seck F, Covarrubias-Pazaran G, Gueye T, Bartholomé J. Realized Genetic Gain in Rice: Achievements from Breeding Programs. RICE (NEW YORK, N.Y.) 2023; 16:61. [PMID: 38099942 PMCID: PMC10724102 DOI: 10.1186/s12284-023-00677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/10/2023] [Indexed: 12/18/2023]
Abstract
Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.
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Affiliation(s)
- Fallou Seck
- Rice Breeding Innovation Platform, International Rice Research Institute, DAPO Box7777, Metro Manila, Philippines
- University Iba Der Thiam of Thiès, GrandStanding, Thiès, Senegal
| | - Giovanny Covarrubias-Pazaran
- Rice Breeding Innovation Platform, International Rice Research Institute, DAPO Box7777, Metro Manila, Philippines
| | - Tala Gueye
- University Iba Der Thiam of Thiès, GrandStanding, Thiès, Senegal
| | - Jérôme Bartholomé
- CIRAD, UMR AGAP, Cali, Colombia.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
- Alliance Bioversity-CIAT, Cali, Colombia.
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Su J, Lu Z, Zeng J, Zhang X, Yang X, Wang S, Zhang F, Jiang J, Chen F. Multi-locus genome-wide association study and genomic prediction for flowering time in chrysanthemum. PLANTA 2023; 259:13. [PMID: 38063918 DOI: 10.1007/s00425-023-04297-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION Multi-locus GWAS detected several known and candidate genes responsible for flowering time in chrysanthemum. The associations could greatly increase the predictive ability of genome selection that accelerates the possible application of GS in chrysanthemum breeding. Timely flowering is critical for successful reproduction and determines the economic value for ornamental plants. To investigate the genetic architecture of flowering time in chrysanthemum, a multi-locus genome-wide association study (GWAS) was performed using a collection of 200 accessions and 330,710 single-nucleotide polymorphisms (SNPs) via 3VmrMLM method. Five flowering time traits including budding (FBD), visible colouring (VC), early opening (EO), full-bloom (OF) and senescing (SF) stages, plus five derived conditional traits were recorded in two environments. Extensive phenotypic variations were observed for these flowering time traits with coefficients of variation ranging from 6.42 to 38.27%, and their broad-sense heritability ranged from 71.47 to 96.78%. GWAS revealed 88 stable quantitative trait nucleotides (QTNs) and 93 QTN-by-environment interactions (QEIs) associated with flowering time traits, accounting for 0.50-8.01% and 0.30-10.42% of the phenotypic variation, respectively. Amongst the genes around these stable QTNs and QEIs, 21 and 10 were homologous to known flowering genes in Arabidopsis; 20 and 11 candidate genes were mined by combining the functional annotation and transcriptomics data, respectively, such as MYB55, FRIGIDA-like, WRKY75 and ANT. Furthermore, genomic selection (GS) was assessed using three models and seven unique marker datasets. We found the prediction accuracy (PA) using significant SNPs identified by GWAS under SVM model exhibited the best performance with PA ranging from 0.90 to 0.95. Our findings provide new insights into the dynamic genetic architecture of flowering time and the identified significant SNPs and candidate genes will accelerate the future molecular improvement of chrysanthemum.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhaowen Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Junwei Zeng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xuefeng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiuwei Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Siyue Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China.
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China.
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Chen Q, Gao K, Xu Y, Sun Y, Pan B, Chen D, Luo C, Cheng X, Liu H, Huang C. Research advance on cold tolerance in chrysanthemum. FRONTIERS IN PLANT SCIENCE 2023; 14:1259229. [PMID: 37828931 PMCID: PMC10565118 DOI: 10.3389/fpls.2023.1259229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Chrysanthemums are one of the top ten most well-known traditional famous flowers in China and one of the top four cut flowers worldwide, holding a significant position in landscape gardening. The cold temperatures of winter restrict the cultivation, introduction, and application of chrysanthemum, resulting in high costs for year-round production. This severely impacts the ornamental and economic value of chrysanthemum. Therefore, research on cold tolerance is of vital importance for guiding chrysanthemum production and application. With the development of genomics, transcriptomics, metabolomics, and other omics approaches, along with high-throughput molecular marker technologies, research on chrysanthemum cold tolerance has been continuously advancing. This article provides a comprehensive overview of the progress in cold tolerance research from various aspects, including chrysanthemum phenotype, physiological mechanisms, the forward genetics, molecular mechanisms, and breeding. The aim is to offer insights into the mechanisms of cold tolerance in chrysanthemum and provide reference for in-depth research and the development of new cold tolerance chrysanthemum varieties.
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Affiliation(s)
- Qingbing Chen
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Kang Gao
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - YuRan Xu
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - YaHui Sun
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Bo Pan
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Dongliang Chen
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chang Luo
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xi Cheng
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hua Liu
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Conglin Huang
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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10
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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2023:S2090-1232(23)00265-5. [PMID: 37739122 DOI: 10.1016/j.jare.2023.09.016] [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: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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11
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Marla S, Felderhoff T, Hayes C, Perumal R, Wang X, Poland J, Morris GP. Genomics and phenomics enabled prebreeding improved early-season chilling tolerance in Sorghum. G3 (BETHESDA, MD.) 2023; 13:jkad116. [PMID: 37232400 PMCID: PMC10411554 DOI: 10.1093/g3journal/jkad116] [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: 02/02/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, chilling sensitivity of sorghum, a tropical-origin cereal crop, limits early planting, and over 50 years of conventional breeding has been stymied by coinheritance of chilling tolerance (CT) loci with undesirable tannin and dwarfing alleles. In this study, phenomics and genomics-enabled approaches were used for prebreeding of sorghum early-season CT. Uncrewed aircraft systems (UAS) high-throughput phenotyping platform tested for improving scalability showed moderate correlation between manual and UAS phenotyping. UAS normalized difference vegetation index values from the chilling nested association mapping population detected CT quantitative trait locus (QTL) that colocalized with manual phenotyping CT QTL. Two of the 4 first-generation Kompetitive Allele Specific PCR (KASP) molecular markers, generated using the peak QTL single nucleotide polymorphisms (SNPs), failed to function in an independent breeding program as the CT allele was common in diverse breeding lines. Population genomic fixation index analysis identified SNP CT alleles that were globally rare but common to the CT donors. Second-generation markers, generated using population genomics, were successful in tracking the donor CT allele in diverse breeding lines from 2 independent sorghum breeding programs. Marker-assisted breeding, effective in introgressing CT allele from Chinese sorghums into chilling-sensitive US elite sorghums, improved early-planted seedling performance ratings in lines with CT alleles by up to 13-24% compared to the negative control under natural chilling stress. These findings directly demonstrate the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.
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Affiliation(s)
- Sandeep Marla
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Terry Felderhoff
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Chad Hayes
- USDA-ARS, Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, Lubbock, TX 79415, USA
| | - Ramasamy Perumal
- Western Kansas Agricultural Research Center, Kansas State University, Hays, KS 67601, USA
| | - Xu Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Department of Agricultural and Biological Engineering, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33598, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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12
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Wang L, Yeo S, Lee M, Endah S, Alhuda NA, Yue GH. Combination of GWAS and F ST-based approaches identified loci associated with economic traits in sugarcane. Mol Genet Genomics 2023:10.1007/s00438-023-02040-2. [PMID: 37289230 DOI: 10.1007/s00438-023-02040-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using FST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Shadame Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - S Endah
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - N A Alhuda
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - G H Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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13
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Sahoo J, Mahanty B, Mishra R, Joshi RK. Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion ( Allium cepa L.) breeding. 3 Biotech 2023; 13:137. [PMID: 37124987 PMCID: PMC10130247 DOI: 10.1007/s13205-023-03562-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
Purple blotch (PB), caused by Alternaria porri (Ellis) Cifferi, is one of the most destructive diseases of onion worldwide. Rapid development and deployment of resistant onion varieties is the most effective approach to control this disease. A single dominant gene, ApR1 was previously linked to PB resistance in onion cultivar 'Arka Kalyan'. In this study, an advanced RIL population derived from a cross between the resistant (Arka Kalyan) and susceptible (Agrifound Rose) cultivar of onion was used to fine map the resistant locus with SNP markers. Twenty plants from the RIL population, ten each with disease resistance and susceptibility trait, were subjected to restriction site-associated DNA sequencing (RAD-Seq) and generated 7388 single nucleotide polymorphisms (SNPs). Correlation analysis between marker genotypes and PB disease phenotype on the 20 plants identified 27 SNPs as candidate markers linked to ApR1 gene for PB resistance. Six candidate SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers designated as ApRsnip5, ApRsnip8, ApRsnip14, ApRsnip21, ApRsnip23 and ApRsnip25. Marker-trait association based on disease phenotyping and KASP genotyping data on 153 RILs confirmed that all six KASP markers were tightly associated with ApR1 gene within the genetic distance of 1.3 CentiMorgan (cM). ApRsnip14 co-segregated with the ApR1 locus. Further, the six KASP markers were tested on 27 onion lines with different genetic backgrounds. ApRsnip14, ApRsnip21, ApRsnip5 and ApRsnip23 not only showed the correct resistance allele in 3 resistance genotypes, but also clustered together in the remaining 24 susceptible lines. Alternatively, ApRsnip8 and ApRsnip25 exhibited false positives in two onion lines which do not have the R-gene. Overall, our results suggest that ApRsnip14 and ApRsnip23 with their close linkage to ApR1 locus and greater applicability on breeding germplasm are recommended in marker-assisted selection for PB resistance in onion breeding program. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03562-7.
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Affiliation(s)
- Jayashree Sahoo
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
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14
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Cruet-Burgos C, Morris GP, Rhodes DH. Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies. BMC PLANT BIOLOGY 2023; 23:165. [PMID: 36977987 PMCID: PMC10045421 DOI: 10.1186/s12870-023-04176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene-the main provitamin A carotenoid-is below the target concentration in sorghum grain, therefore biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors. RESULTS In this study, we characterized carotenoids in 446 accessions from the sorghum association panel and carotenoid panel using high-performance liquid chromatography, finding high carotenoid accessions not previously identified. Genome-wide association studies conducted with 345 accessions, confirmed that zeaxanthin epoxidase is a major gene underlying variation for not only zeaxanthin, but also lutein and β-carotene. High carotenoid lines were found to have limited genetic diversity, and originated predominantly from only one country. Potential novel genetic diversity for carotenoid content was identified through genomic predictions in 2,495 accessions of unexplored germplasm. Oligogenic variation of carotenoids was confirmed, as well as evidence for polygenic variation, suggesting both marker-assisted selection and genomic selection can facilitate breeding efforts. CONCLUSIONS Sorghum vitamin A biofortification could be beneficial for millions of people who rely on it as a dietary staple. Carotenoid content in sorghum is low, but high heritability suggests that increasing concentrations through breeding is possible. Low genetic diversity among high carotenoid lines might be the main limitation for breeding efforts, therefore further germplasm characterization is needed to assess the feasibility of biofortification breeding. Based on germplasm here evaluated, most countries' germplasm lacks high carotenoid alleles, thus pre-breeding will be needed. A SNP marker within the zeaxanthin epoxidase gene was identified as a good candidate for use in marker-assisted selection. Due to the oligogenic and polygenic variation of sorghum grain carotenoids, both marker-assisted selection and genomic selection can be employed to accelerate breeding efforts.
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Affiliation(s)
- Clara Cruet-Burgos
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Geoffrey P Morris
- Department of Soil & Crop Science, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Davina H Rhodes
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
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15
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Kumar M, Singh RP, Jena D, Singh V, Rout D, Arsode PB, Choudhary M, Singh P, Chahar S, Samantaray S, Mukherjee AK, Mohan C, Bohra A, Das G, Balo S, Singh ON, Verma R. Marker-Assisted Improvement for Durable Bacterial Blight Resistance in Aromatic Rice Cultivar HUR 917 Popular in Eastern Parts of India. PLANTS (BASEL, SWITZERLAND) 2023; 12:1363. [PMID: 36987051 PMCID: PMC10058408 DOI: 10.3390/plants12061363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/10/2022] [Accepted: 12/16/2022] [Indexed: 06/19/2023]
Abstract
Bacterial blight (BB) is a devastating disease of rice in the tropics of Indian sub-continent, where the presence of Xoo races with varying levels of genetic diversity and virulence renders disease management extremely challenging. In this context, marker-assisted improvement of plant resistance has been proven as one of the most promising approaches for the development of sustainable rice cultivars. The present study demonstrates the marker-assisted introgression of the three BB resistant genes (Xa21 + xa13 + xa5) into the background of HUR 917, a popular aromatic short grain (ASG) rice cultivar in India. The performance of the resulting improved products (near isogenic lines (NILs), HR 23-5-37-83-5, HR 23-5-37-121-10, HR 23-5-37-121-14, HR 23-65-6-191-13, HR 23-65-6-237-2, HR 23-65-6-258-10 and HR 23-65-6-258-21) establishes the utility of marker-assisted selection (MAS) approach for accelerated trait introgression in rice. The MAS-bred lines carrying three introgressed genes showed broad spectrum BB resistance (lesion length, LL of 1.06 ± 1.35 cm to 4.61 ± 0.87 cm). Besides, these improved lines showed the complete product profile of recurrent parent HUR 917 along with the enhanced level of durable BB resistance. The improved introgression lines with durable BB resistance would contribute to sustainable rice production in India, particularly in the Indo-Gangetic plane that has substantial acreage under HUR 917.
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Affiliation(s)
- Manish Kumar
- Institute of Agricultural Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ravi Pratap Singh
- Institute of Agricultural Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Debarchana Jena
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Vineeta Singh
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Diptibala Rout
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | | | - Madhu Choudhary
- Institute of Agricultural Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Prakash Singh
- Veer Kunwar Singh College of Agriculture, Bihar Agricultural University-BAU, Sabaur, Dumraon, Buxar 802136, Bihar, India
| | - Suman Chahar
- Central State Farm, National Seeds Corporation, Sirsa Road, Hisar 125001, Haryana, India
| | | | | | - Chander Mohan
- Department of Agriculture, Cooperation and Farmers Welfare, Government of India, New Delhi 110001, Delhi, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre (SABC) and Centre for Crop and Food Innovation (CCFI), Murdoch University, Perth, WA 6150, Australia
| | - Goutam Das
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - Sumana Balo
- Department of Soil Science and Agricultural Chemistry, Uttar Banga Krishi Vishwavidyalaya, Coochbehar 736165, West Bengal, India
| | - Onkar Nath Singh
- Birsa Agricultural University (BAU), Ranchi 834006, Jharkhand, India
| | - Ramlakhan Verma
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
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16
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Hernandez CO, Labate J, Reitsma K, Fabrizio J, Bao K, Fei Z, Grumet R, Mazourek M. Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections. FRONTIERS IN PLANT SCIENCE 2023; 14:1130814. [PMID: 36993863 PMCID: PMC10040574 DOI: 10.3389/fpls.2023.1130814] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.
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Affiliation(s)
- Christopher O. Hernandez
- Department of Agriculture Nutrition and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Joanne Labate
- Plant Genetic Resource Conservation Unit, United States Department of Agricultural Research Service, Geneva, NY, United States
| | - Kathleen Reitsma
- North Central Regional Plant Introduction Station, Iowa State University, Ames, IA, United States
| | - Jack Fabrizio
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- U.S. Department of Agriculture-Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Michael Mazourek
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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17
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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18
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Identification of quantitative trait loci for growth traits in red swamp crayfish (Procambarus clarkii). AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Arriagada O, Arévalo B, Cabeza RA, Carrasco B, Schwember AR. Meta-QTL Analysis for Yield Components in Common Bean ( Phaseolus vulgaris L.). PLANTS (BASEL, SWITZERLAND) 2022; 12:117. [PMID: 36616246 PMCID: PMC9824219 DOI: 10.3390/plants12010117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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20
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Li X, Wei Y, Ma Y, Cao G, Ma S, Zhang T, Zhan Z, Piao Z. Marker-Assisted Pyramiding of CRa and CRd Genes to Improve the Clubroot Resistance of Brassica rapa. Genes (Basel) 2022; 13:genes13122414. [PMID: 36553679 PMCID: PMC9777773 DOI: 10.3390/genes13122414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an economically important soil-borne disease that threatens Brassicaceae crops worldwide. In recent years, the incidence area of Chinese cabbage (Brassica rapa ssp. pekinensis) clubroot disease has increased, which severely affects the yield and quality of Chinese cabbage. The resistance of varieties harboring the single clubroot-resistance (CR) gene is easily broken through by P. brassicae pathotypes. CRa and CRd, genetically identified in B. rapa, are CR genes known to be highly resistant to different P. brassicaea pathotypes. In our study, we perform the gene pyramiding of CRa and CRd in Chinese cabbages through marker-assisted selection (MAS), and develop homozygous pyramided lines. The newly generated pyramided lines exhibit greater resistance to six different pathotypes than that of two parental lines carrying a single CR gene. This study provides new CR-gene-pyramided lines for the development of clubroot-resistant Brassica varieties for future breeding programs.
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21
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Gomes-Messias LM, Vianello RP, Marinho GR, Rodrigues LA, Coelho AG, Pereira HS, Melo LC, de Souza TLPO. Genetic mapping of the Andean anthracnose resistance gene present in the common bean cultivar BRSMG Realce. FRONTIERS IN PLANT SCIENCE 2022; 13:1033687. [PMID: 36507385 PMCID: PMC9728541 DOI: 10.3389/fpls.2022.1033687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
The rajado seeded Andean bean (Phaseolus vulgaris L.) cultivar BRSMG Realce (striped seed coat) developed by Embrapa expressed a high level of anthracnose resistance, caused by Colletotrichum lindemuthianum, in field and greenhouse screenings. The main goal of this study was to evaluate the inheritance of anthracnose resistance in BRSMG Realce, map the resistance locus or major gene cluster previously named as Co-Realce, identify resistance-related positional genes, and analyze potential markers linked to the resistance allele. F2 plants derived from the cross BRSMG Realce × BRS FC104 (Mesoamerican) and from the cross BRSMG Realce × BRS Notável (Mesoamerican) were inoculated with the C. lindemuthianum races 475 and 81, respectively. The BRSMG Realce × BRS FC104 F2 population was also genotyped using the DArTseq technology. Crosses between BRSMG Realce and BAT 93 (Mesoamerican) were also conducted and resulting F2 plants were inoculated with the C. lindemuthianum races 65 and 1609, individually. The results shown that anthracnose resistance in BRSMG Realce is controlled by a single locus with complete dominance. A genetic map including 1,118 SNP markers was built and shown 78% of the markers mapped at a distances less than 5.0 cM, with a total genetic length of 4,473.4 cM. A major locus (Co-Realce) explaining 54.6% of the phenotypic variation of symptoms caused by the race 475 was identified in Pv04, flanked by the markers snp1327 and snp12782 and 4.48 cM apart each other. These SNPs are useful for marker-assisted selection, due to an estimated selection efficiency of 99.2%. The identified resistance allele segregates independently of the resistance allele Co-33 (Pv04) present in BAT 93. The mapped genomic region with 704,867 bp comprising 63 putative genes, 44 of which were related to the pathogen-host interaction. Based on all these results and evidence, anthracnose resistance in BRSMG Realce should be considered as monogenic, useful for breeding purpose. It is proposed that locus Co-Realce is unique and be provisionally designated as CoPv04R until be officially nominated in accordance with the rules established by the Bean Improvement Cooperative Genetics Committee.
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22
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Elbasyoni IS, Eltaher S, Morsy S, Mashaheet AM, Abdallah AM, Ali HG, Mariey SA, Baenziger PS, Frels K. Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley. PLANTS (BASEL, SWITZERLAND) 2022; 11:3072. [PMID: 36432800 PMCID: PMC9696095 DOI: 10.3390/plants11223072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI.
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Affiliation(s)
- Ibrahim S. Elbasyoni
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Shamseldeen Eltaher
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Sadat City 32897, Egypt
| | - Sabah Morsy
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Alsayed M. Mashaheet
- Plant Pathology Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Ahmed M. Abdallah
- Natural Resources and Agricultural Engineering Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Heba G. Ali
- Barley Research Department, Field Crops Research Institute, Agricultural Research Center, 9 Gamma Street-Giza, Cairo 12619, Egypt
| | - Samah A. Mariey
- Barley Research Department, Field Crops Research Institute, Agricultural Research Center, 9 Gamma Street-Giza, Cairo 12619, Egypt
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Katherine Frels
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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23
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Rathour R, Kumar R, Thakur K, Pote TD. Genetic improvement for blast resistance in high-yielding cold-tolerant rice ( Oryza sativa L.) cultivar Himalaya 741 by marker-assisted backcross breeding. 3 Biotech 2022; 12:165. [PMID: 35845107 PMCID: PMC9276897 DOI: 10.1007/s13205-022-03244-w] [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: 09/15/2021] [Accepted: 06/25/2022] [Indexed: 11/28/2022] Open
Abstract
Blast disease and cold stress are two major yield-limiting factors for rice under temperate climates. Marker-assisted backcross breeding approach (MABB) was employed for the improvement of blast resistance in a popular cold-tolerant variety 'Himalaya741' by introgressing a broad-spectrum resistance locus Pi9 from a Basmati donor PB1637. A combined use of phenotypic selection and marker-based genotypic selection ensured speedy reconstitution of the recurrent parent genome (RPG) in backcross progenies; RPG recovery in most of the progenies was > 96% with three progenies namely, HPU-1-33, -38 and -49 showing complete recovery of recurrent parent genome. Notwithstanding a very higher recovery rate of RPG in introgression lines, the lines still inherited a large linkage block > 13.3 Mb with Pi9 from the donor line PB1637. The donor chromosome segments co-inherited with Pi9 gene, however, did not have any adverse effect on the agronomic performance of the Pi9 introgression lines. Of the eight genetically superior Pi9 introgression lines identified, two exhibited resemblance to Himalaya 741 for most of the agronomic traits in addition to having superior grain length and tiller number. The introgression line HPU-1-81 displayed 44% yield superiority over recurrent parent, primarily due to improvement in yield-contributing traits, namely, tiller number, panicle length, thousand-seed-weight and grain length. All the Pi9 introgression lines displayed a high level of resistance comparable to PB1637 against two highly virulent blast races, which collectively displayed compatibility to 15 different major resistance genes. The introgression lines also possessed reproductive stage cold tolerance similar to recurrent parent under prevailing cold stress conditions. The agronomically superior Pi9 introgression lines developed herein are expected to provide a comparable or better substitute to blast susceptible variety Himalaya 741 for extenuating losses due to cold stress and blast disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03244-w.
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Affiliation(s)
- Rajeev Rathour
- CSK Himachal Pradesh Agricultural University, Palampur, 176062 India
| | - Rohit Kumar
- CSK Himachal Pradesh Agricultural University, Palampur, 176062 India
| | - Kalpna Thakur
- CSK Himachal Pradesh Agricultural University, Palampur, 176062 India
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24
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Malhotra N, Sharma P, Sood H, Chandora R, Arya M, Rana JC, Singh M. Agro-Morphological Characterization and Nutritional Profiling of Traditional Himalayan Crop Landraces for Their Promotion Toward Mainstream Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:898220. [PMID: 35812955 PMCID: PMC9258745 DOI: 10.3389/fpls.2022.898220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The northwest Indian Himalayas are often regarded as a biological hotspot for the presence of rich agro-biodiversity harboring locally adapted traditional crop landraces facing utter neglect owing to modern agricultural systems promoting high-yielding varieties. Addressing this challenge requires extricating the potential of such cultivars in terms of agro-morphological and nutritional attributes. In this study, 29 traditional crop landraces of maize (11), paddy (07), finger millet (03), buckwheat (05), and naked barley (03) were characterized and evaluated for target traits of interest. In maize, Chitkanu emerged as an early maturing landrace (107 days) with high concentrations of zinc (Zn), iron (Fe), and potassium (K), and Safed makki showed the highest 100-seed weight (28.20 g). Similarly, Bamkua dhan exhibited high concentrations of K and phosphorus (P), and Lamgudi dhan showed a high protein content (14.86 g/100 g) among paddy landraces. Ogla-I and Phapra-I showed high contents of protein (14.80 g/100 g) and flavonoids (20.50 mg/g) among buckwheat landraces, respectively, followed by Nei-I, which exhibited the highest protein content (15.66 g/100 g) among naked barley landraces. Most of the target traits varied significantly (p < 0.05) among evaluated samples, except those associated with finger millet landraces. The grouping pattern obtained by principal component analysis (PCA) and multidimensional scaling (MDS) was congruent with the geographical relationship among the crop landraces. This study led to the identification of elite crop landraces having useful variations that could be exploited in plant breeding programs and biofortification strategies for future crop improvement. Our endeavor would aid in conserving the depleting Himalayan agro-biodiversity and promoting versatile traditional crops toward mainstream agriculture vis-à-vis future nutritional security.
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Affiliation(s)
- Nikhil Malhotra
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Shimla, India
| | - Paras Sharma
- Indian Council of Medical Research (ICMR)-National Institute of Nutrition, Hyderabad, India
| | - Hemant Sood
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, India
| | - Rahul Chandora
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Shimla, India
| | - Mamta Arya
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Bhowali, India
| | - Jai Chand Rana
- Alliance of Bioversity International and CIAT, New Delhi, India
| | - Mohar Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Shimla, India
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25
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Proud C, Campbell B, Susanti Z, Fukai S, Godwin I, Ovenden B, Snell P, Mitchell J. Quantitative trait loci (QTL) for low temperature tolerance at the young microspore stage in rice ( Oryza sativa L.) in Australian breeding material. BREEDING SCIENCE 2022; 72:238-247. [PMID: 36408321 PMCID: PMC9653190 DOI: 10.1270/jsbbs.21096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6, qYMCT6.1, in which the Australian variety, Kyeema, was the donor for increased fertility. Additional five genomics regions were identified that co-located with previously reported QTL, two of which have been previously cloned. Additionally, for the first time a QTL for spikelet fertility qYMCT10.1, has been shown to co-locate with the number of dehisced anthers qYMCTF10.1 which increases the shedding of pollen from the anthers. This study revealed one new QTL for low temperature tolerance at YMS in temperate japonica germplasm and identified an additional five previously reported. These QTL will be utilised for MAS in the Australian rice breeding program and may have merit for temperate breeding programs globally.
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Affiliation(s)
- Christopher Proud
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Bradley Campbell
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Zuziana Susanti
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
- Indonesian Centre for Rice Research, Agency for Agricultural Research and Development, Subang, West-Java, Indonesia
| | - Shu Fukai
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ben Ovenden
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW 2703, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW 2703, Australia
| | - Jaquie Mitchell
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
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Vinarao R, Proud C, Snell P, Fukai S, Mitchell J. Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice ( Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109. FRONTIERS IN PLANT SCIENCE 2022; 13:873677. [PMID: 35574104 PMCID: PMC9100824 DOI: 10.3389/fpls.2022.873677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.
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Affiliation(s)
- Ricky Vinarao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher Proud
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, Australia
| | - Shu Fukai
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jaquie Mitchell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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27
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Saini DK, Srivastava P, Pal N, Gupta PK. Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1049-1081. [PMID: 34985537 DOI: 10.1007/s00122-021-04018-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/10/2021] [Indexed: 05/03/2023]
Abstract
In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder's MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified. Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999-2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder's MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
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28
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Marker-Assisted Pyramiding of Genes for Multilocular Ovaries, Self-Compatibility, and Clubroot Resistance in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molecular marker-assisted gene pyramiding combined with backcrossing has been widely applied for crop variety improvement. Molecular marker identification could be used in the early stage of breeding to achieve the rapid and effective pyramiding of multiple genes. To create high-quality germplasm for Chinese cabbage breeding, multi-gene pyramiding for self-compatibility, multilocular, and clubroot resistance was performed through molecular marker-assisted selection. The results showed that self-compatibility and multilocular traits were controlled by a pair of recessive genes. Two flanking markers, sau_um190 and cun_246a, and marker Teo-1, based on the gene sequence related to multilocular ovaries, were used for multilocular ovary trait selection. Two flanking markers, SCF-6 and SC-12, and marker Sal-SLGI /PK1+PK4, based on the gene sequence, were used for self-compatibility selection. Two flanking markers, TCR74 and TCR79, closely linked to clubroot resistance gene CRb, were used as foreground selection markers. Based on Chinese cabbage genomic information, 111 SSR markers covering 10 chromosomes were applied for background selection. After multiple generations of selection, a multi-gene pyramided line from a BC4F2 population with self-compatibility, multilocular ovaries, and clubroot resistance was obtained with a high genomic background recovery rate. The improved pyramided line is expected to be utilized as a potential material in further breeding programs.
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Sandhu KS, Patil SS, Aoun M, Carter AH. Multi-Trait Multi-Environment Genomic Prediction for End-Use Quality Traits in Winter Wheat. Front Genet 2022; 13:831020. [PMID: 35173770 PMCID: PMC8841657 DOI: 10.3389/fgene.2022.831020] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/06/2022] [Indexed: 11/13/2022] Open
Abstract
Soft white wheat is a wheat class used in foreign and domestic markets to make various end products requiring specific quality attributes. Due to associated cost, time, and amount of seed needed, phenotyping for the end-use quality trait is delayed until later generations. Previously, we explored the potential of using genomic selection (GS) for selecting superior genotypes earlier in the breeding program. Breeders typically measure multiple traits across various locations, and it opens up the avenue for exploring multi-trait-based GS models. This study's main objective was to explore the potential of using multi-trait GS models for predicting seven different end-use quality traits using cross-validation, independent prediction, and across-location predictions in a wheat breeding program. The population used consisted of 666 soft white wheat genotypes planted for 5 years at two locations in Washington, United States. We optimized and compared the performances of four uni-trait- and multi-trait-based GS models, namely, Bayes B, genomic best linear unbiased prediction (GBLUP), multilayer perceptron (MLP), and random forests. The prediction accuracies for multi-trait GS models were 5.5 and 7.9% superior to uni-trait models for the within-environment and across-location predictions. Multi-trait machine and deep learning models performed superior to GBLUP and Bayes B for across-location predictions, but their advantages diminished when the genotype by environment component was included in the model. The highest improvement in prediction accuracy, that is, 35% was obtained for flour protein content with the multi-trait MLP model. This study showed the potential of using multi-trait-based GS models to enhance prediction accuracy by using information from previously phenotyped traits. It would assist in speeding up the breeding cycle time in a cost-friendly manner.
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Affiliation(s)
- Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Shruti Sunil Patil
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, United States1
| | - Meriem Aoun
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Arron H. Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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Bartholomé J, Prakash PT, Cobb JN. Genomic Prediction: Progress and Perspectives for Rice Improvement. Methods Mol Biol 2022; 2467:569-617. [PMID: 35451791 DOI: 10.1007/978-1-0716-2205-6_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genomic prediction can be a powerful tool to achieve greater rates of genetic gain for quantitative traits if thoroughly integrated into a breeding strategy. In rice as in other crops, the interest in genomic prediction is very strong with a number of studies addressing multiple aspects of its use, ranging from the more conceptual to the more practical. In this chapter, we review the literature on rice (Oryza sativa) and summarize important considerations for the integration of genomic prediction in breeding programs. The irrigated breeding program at the International Rice Research Institute is used as a concrete example on which we provide data and R scripts to reproduce the analysis but also to highlight practical challenges regarding the use of predictions. The adage "To someone with a hammer, everything looks like a nail" describes a common psychological pitfall that sometimes plagues the integration and application of new technologies to a discipline. We have designed this chapter to help rice breeders avoid that pitfall and appreciate the benefits and limitations of applying genomic prediction, as it is not always the best approach nor the first step to increasing the rate of genetic gain in every context.
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Affiliation(s)
- Jérôme Bartholomé
- CIRAD, UMR AGAP Institut, Montpellier, France.
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France.
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines.
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Heredia MC, Kant J, Prodhan MA, Dixit S, Wissuwa M. Breeding rice for a changing climate by improving adaptations to water saving technologies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:17-33. [PMID: 34218290 DOI: 10.1007/s00122-021-03899-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
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Affiliation(s)
| | | | - M Asaduzzaman Prodhan
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, The Philippines
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
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Arriagada O, Gadaleta A, Marcotuli I, Maccaferri M, Campana M, Reveco S, Alfaro C, Matus I, Schwember AR. A comprehensive meta-QTL analysis for yield-related traits of durum wheat ( Triticum turgidum L. var. durum) grown under different water regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:984269. [PMID: 36147234 PMCID: PMC9486101 DOI: 10.3389/fpls.2022.984269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 05/13/2023]
Abstract
Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matteo Campana
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samantha Reveco
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Alfaro
- Centro Regional Rayentue, Instituto de Investigaciones Agropecuarias (INIA), Rengo, Chile
| | - Iván Matus
- Centro Regional Quilamapu, Instituto de Investigaciones Agropecuarias (INIA), Chillán, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Andrés R. Schwember,
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González Guzmán M, Cellini F, Fotopoulos V, Balestrini R, Arbona V. New approaches to improve crop tolerance to biotic and abiotic stresses. PHYSIOLOGIA PLANTARUM 2022; 174:e13547. [PMID: 34480798 PMCID: PMC9290814 DOI: 10.1111/ppl.13547] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 05/24/2023]
Abstract
During the last years, a great effort has been dedicated at the development and employment of diverse approaches for achieving more stress-tolerant and climate-flexible crops and sustainable yield increases to meet the food and energy demands of the future. The ongoing climate change is in fact leading to more frequent extreme events with a negative impact on food production, such as increased temperatures, drought, and soil salinization as well as invasive arthropod pests and diseases. In this review, diverse "green strategies" (e.g., chemical priming, root-associated microorganisms), and advanced technologies (e.g., genome editing, high-throughput phenotyping) are described on the basis of the most recent research evidence. Particularly, attention has been focused on the potential use in a context of sustainable and climate-smart agriculture (the so called "next agriculture generation") to improve plant tolerance and resilience to abiotic and biotic stresses. In addition, the gap between the results obtained in controlled experiments and those from application of these technologies in real field conditions (lab to field step) is also discussed.
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Affiliation(s)
- Miguel González Guzmán
- Departament de Ciències Agràries i del Medi NaturalUniversitat Jaume ICastelló de la PlanaSpain
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
| | - Francesco Cellini
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (ALSIA)MetapontoItaly
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante (CNR, IPSP)TorinoItaly
| | - Vasileios Fotopoulos
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Department of Agricultural Sciences, Biotechnology & Food ScienceCyprus University of TechnologyLemesosCyprus
| | - Raffaella Balestrini
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante (CNR, IPSP)TorinoItaly
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi NaturalUniversitat Jaume ICastelló de la PlanaSpain
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
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Discovery of a Novel Leaf Rust ( Puccinia recondita) Resistance Gene in Rye ( Secale cereale L.) Using Association Genomics. Cells 2021; 11:cells11010064. [PMID: 35011626 PMCID: PMC8750363 DOI: 10.3390/cells11010064] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/22/2022] Open
Abstract
Leaf rust constitutes one of the most important foliar diseases in rye (Secale cereale L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gülzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019. We observed lines with high leaf rust resistance efficacy at all locations in both years. A genome-wide association study using 261,406 informative single-nucleotide polymorphisms revealed two genomic regions associated with resistance on chromosome arms 1RS and 7RS, respectively. The most resistance-associated marker on chromosome arm 1RS physically co-localized with molecular markers delimiting Pr3. In the reference genomes Lo7 and Weining, the genomic region associated with resistance on chromosome arm 7RS contained a large number of nucleotide-binding leucine-rich repeat (NLR) genes. Residing in close proximity to the most resistance-associated marker, we identified a cluster of NLRs exhibiting close protein sequence similarity with the wheat leaf rust Lr1 gene situated on chromosome arm 5DL in wheat, which is syntenic to chromosome arm 7RS in rye. Due to the close proximity to the most resistance-associated marker, our findings suggest that the considered leaf rust R gene, provisionally denoted Pr6, could be a Lr1 ortholog in rye.
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Singh A, Roychoudhury A. Gene regulation at transcriptional and post-transcriptional levels to combat salt stress in plants. PHYSIOLOGIA PLANTARUM 2021; 173:1556-1572. [PMID: 34260753 DOI: 10.1111/ppl.13502] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/24/2021] [Accepted: 07/14/2021] [Indexed: 05/27/2023]
Abstract
Soil salinity is a major challenge that will be faced more and more by human population in the near future. Higher salt concentrations in the soil limit the growth and production of crops, which poses serious threats to global food production. Various plant breeding approaches have been followed in the past which are reported to reduce the effect of salt stress by inducing the level of protective metabolites like osmolytes and antioxidants. Conventional breeding approaches are time-consuming and not cost-effective. In recent times, genetic engineering has been largely followed to confer salt tolerance through introgressions of single transgenes or stacking multiple transgenes. However, most of such works are limited only at the laboratory level and field trials are still awaited to prove the long-term efficacy of such transgenics. In this review, we attempt to present a broad overview of the current strategies undertaken to develop halophytic and salt-tolerant crops. The salt-induced damages in the plants are highlighted, followed by representing the novel traits, associated with salt stress, which can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of transcriptional and epigenetic regulation in plants for amelioration of salt-induced damages has been reviewed. The role of post-transcriptional mechanisms such as microRNA regulation, genome editing and alternative splicing, during salt stress, and their implications in the development of salt-tolerant crops are also discussed. Finally, we present a short overview about the role of ion transporters and rhizobacteria in the engineering of salt tolerance in crop species.
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Affiliation(s)
- Ankur Singh
- Post-Graduate Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Aryadeep Roychoudhury
- Post-Graduate Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
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Juma RU, Bartholomé J, Thathapalli Prakash P, Hussain W, Platten JD, Lopena V, Verdeprado H, Murori R, Ndayiragije A, Katiyar SK, Islam MR, Biswas PS, Rutkoski JE, Arbelaez JD, Mbute FN, Miano DW, Cobb JN. Identification of an Elite Core Panel as a Key Breeding Resource to Accelerate the Rate of Genetic Improvement for Irrigated Rice. RICE (NEW YORK, N.Y.) 2021; 14:92. [PMID: 34773509 PMCID: PMC8590642 DOI: 10.1186/s12284-021-00533-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Rice genetic improvement is a key component of achieving and maintaining food security in Asia and Africa in the face of growing populations and climate change. In this effort, the International Rice Research Institute (IRRI) continues to play a critical role in creating and disseminating rice varieties with higher productivity. Due to increasing demand for rice, especially in Africa, there is a strong need to accelerate the rate of genetic improvement for grain yield. In an effort to identify and characterize the elite breeding pool of IRRI's irrigated rice breeding program, we analyzed 102 historical yield trials conducted in the Philippines during the period 2012-2016 and representing 15,286 breeding lines (including released varieties). A mixed model approach based on the pedigree relationship matrix was used to estimate breeding values for grain yield, which ranged from 2.12 to 6.27 t·ha-1. The rate of genetic gain for grain yield was estimated at 8.75 kg·ha-1 year-1 (0.23%) for crosses made in the period from 1964 to 2014. Reducing the data to only IRRI released varieties, the rate doubled to 17.36 kg·ha-1 year-1 (0.46%). Regressed against breeding cycle the rate of gain for grain yield was 185 kg·ha-1 cycle-1 (4.95%). We selected 72 top performing lines based on breeding values for grain yield to create an elite core panel (ECP) representing the genetic diversity in the breeding program with the highest heritable yield values from which new products can be derived. The ECP closely aligns with the indica 1B sub-group of Oryza sativa that includes most modern varieties for irrigated systems. Agronomic performance of the ECP under multiple environments in Asia and Africa confirmed its high yield potential. We found that the rate of genetic gain for grain yield found in this study was limited primarily by long cycle times and the direct introduction of non-improved material into the elite pool. Consequently, the current breeding scheme for irrigated rice at IRRI is based on rapid recurrent selection among highly elite lines. In this context, the ECP constitutes an important resource for IRRI and NAREs breeders to carefully characterize and manage that elite diversity.
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Affiliation(s)
- Roselyne U Juma
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- Kenya Agricultural and Livestock Research Organization, 50100-169, Kakamega, Kenya
| | - Jérôme Bartholomé
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines.
- AGAP Institut, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | - Parthiban Thathapalli Prakash
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
| | - Waseem Hussain
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
| | - John D Platten
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
| | - Vitaliano Lopena
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
| | - Holden Verdeprado
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
| | - Rosemary Murori
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- International Rice Research Institute (IRRI) C/O ILRI, Old Naivasha Road, PO Box 30709, 00100, Nairobi, Kenya
| | - Alexis Ndayiragije
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- Institiuto de Investigação de Moçambique (IIAM), Av. das FPLM nr 2698, Recinto do IIAM, Maputo, Mozambique
| | - Sanjay Kumar Katiyar
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- International Rice Research Institute, South Asia Hub, ICRISAT, Hyderabad, 502324, India
| | - Md Rafiqul Islam
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- Bangladesh Office, International Rice Research Institute (IRRI), Dhaka, Bangladesh
| | - Partha S Biswas
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Jessica E Rutkoski
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- University of Illinois at Urbana-Champaign, Urbana, USA, Illinois
| | - Juan D Arbelaez
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines
- University of Illinois at Urbana-Champaign, Urbana, USA, Illinois
| | - Felister N Mbute
- Department of Plant Science and Crop Protection, University of Nairobi, PO Box 29053, 00625, Kangemi, Kenya
| | - Douglas W Miano
- Department of Plant Science and Crop Protection, University of Nairobi, PO Box 29053, 00625, Kangemi, Kenya
| | - Joshua N Cobb
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Los Baños, Metro, DAPO Box 7777, Manila, Philippines.
- RiceTec. Inc, PO Box 1305, Alvin, TX, 77512, USA.
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Steady agronomic and genetic interventions are essential for sustaining productivity in intensive rice cropping. Proc Natl Acad Sci U S A 2021; 118:2110807118. [PMID: 34740974 PMCID: PMC8609317 DOI: 10.1073/pnas.2110807118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 11/25/2022] Open
Abstract
Steady agronomic and genetic interventions helped sustain high annual rice production in an intensive irrigated monoculture system under a changing climate. However, the system did not achieve the increases in yield required to keep pace with the growing global demand for rice because annual yield potential was stagnant, and apparent biotic constraints limited yield in the wet season. Intensive systems with two or three rice (Oryza sativa L.) crops per year account for about 50% of the harvested area for irrigated rice in Asia. Any reduction in productivity or sustainability of these systems has serious implications for global food security. Rice yield trends in the world’s longest-running long-term continuous cropping experiment (LTCCE) were evaluated to investigate consequences of intensive cropping and to draw lessons for sustaining production in Asia. Annual production was sustained at a steady level over the 50-y period in the LTCCE through continuous adjustment of management practices and regular cultivar replacement. Within each of the three annual cropping seasons (dry, early wet, and late wet), yield decline was observed during the first phase, from 1968 to 1990. Agronomic improvements in 1991 to 1995 helped to reverse this yield decline, but yield increases did not continue thereafter from 1996 to 2017. Regular genetic and agronomic improvements were sufficient to maintain yields at steady levels in dry and early wet seasons despite a reduction in the yield potential due to changing climate. Yield declines resumed in the late wet season. Slower growth in genetic gain after the first 20 y was associated with slower breeding cycle advancement as indicated by pedigree depth. Our findings demonstrate that through adjustment of management practices and regular cultivar replacement, it is possible to sustain a high level of annual production in irrigated systems under a changing climate. However, the system was unable to achieve further increases in yield required to keep pace with the growing global rice demand.
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Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-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: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
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Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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Malenica N, Dunić JA, Vukadinović L, Cesar V, Šimić D. Genetic Approaches to Enhance Multiple Stress Tolerance in Maize. Genes (Basel) 2021; 12:genes12111760. [PMID: 34828366 PMCID: PMC8617808 DOI: 10.3390/genes12111760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time.
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Affiliation(s)
- Nenad Malenica
- Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia;
| | - Jasenka Antunović Dunić
- Department of Biology, Josip Juraj Strossmayer University, Cara Hadrijana 8/A, 31000 Osijek, Croatia; (J.A.D.); (V.C.)
| | - Lovro Vukadinović
- Agricultural Institute Osijek, Južno Predgrađe 17, 31000 Osijek, Croatia;
| | - Vera Cesar
- Department of Biology, Josip Juraj Strossmayer University, Cara Hadrijana 8/A, 31000 Osijek, Croatia; (J.A.D.); (V.C.)
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Domagoj Šimić
- Agricultural Institute Osijek, Južno Predgrađe 17, 31000 Osijek, Croatia;
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska 25, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-31-515-521
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Vinarao R, Proud C, Snell P, Fukai S, Mitchell J. QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems. PLANTS (BASEL, SWITZERLAND) 2021; 10:2099. [PMID: 34685908 PMCID: PMC8537842 DOI: 10.3390/plants10102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3-17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7-15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4's effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.
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Affiliation(s)
- Ricky Vinarao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
| | - Christopher Proud
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW 2703, Australia;
| | - Shu Fukai
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
| | - Jaquie Mitchell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
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Saini DK, Chopra Y, Pal N, Chahal A, Srivastava P, Gupta PK. Meta-QTLs, ortho-MQTLs and candidate genes for nitrogen use efficiency and root system architecture in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2245-2267. [PMID: 34744364 PMCID: PMC8526679 DOI: 10.1007/s12298-021-01085-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
In wheat, meta-QTLs (MQTLs), ortho-MQTLs, and candidate genes (CGs) were identified for nitrogen use efficiency and root system architecture. For this purpose, 1788 QTLs were available from 24 studies published during 2006-2020. Of these, 1098 QTLs were projected onto the consensus map resulting in 118 MQTLs. The average confidence interval (CI) of MQTLs was reduced up to 8.56 folds in comparison to the average CI of QTLs. Of the 118 MQTLs, 112 were anchored to the physical map of the wheat reference genome. The physical interval of MQTLs ranged from 0.02 to 666.18 Mb with a mean of 94.36 Mb. Eighty-eight of these 112 MQTLs were verified by marker-trait associations (MTAs) identified in published genome-wide association studies (GWAS); the MQTLs that were verified using GWAS also included 9 most robust MQTLs, which are particularly useful for breeders; we call them 'Breeder's QTLs'. Some selected wheat MQTLs were further utilized for the identification of ortho-MQTLs for wheat and maize; 9 such ortho-MQTLs were available. As many as 1991 candidate genes (CGs) were also detected, which included 930 CGs with an expression level of > 2 transcripts per million in relevant organs/tissues. Among the CGs, 97 CGs with functions previously reported as important for the traits under study were selected. Based on homology analysis and expression patterns, 49 orthologues of 35 rice genes were also identified in MQTL regions. The results of the present study may prove useful for the improvement of selection strategy for yield potential, stability, and performance under N-limiting conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01085-0.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
- Present Address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Venezia M, Creasey Krainer KM. Current Advancements and Limitations of Gene Editing in Orphan Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:742932. [PMID: 34630494 PMCID: PMC8493294 DOI: 10.3389/fpls.2021.742932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 05/23/2023]
Abstract
Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world's most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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Vitale P, Fania F, Esposito S, Pecorella I, Pecchioni N, Palombieri S, Sestili F, Lafiandra D, Taranto F, De Vita P. QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents. Genes (Basel) 2021; 12:genes12040604. [PMID: 33923933 PMCID: PMC8074140 DOI: 10.3390/genes12040604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023] Open
Abstract
Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.
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Affiliation(s)
- Paolo Vitale
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Fabio Fania
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Samuela Palombieri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, Italy
- Correspondence: (F.T.); (P.D.V.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
- Correspondence: (F.T.); (P.D.V.)
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Balestrini R, Brunetti C, Cammareri M, Caretto S, Cavallaro V, Cominelli E, De Palma M, Docimo T, Giovinazzo G, Grandillo S, Locatelli F, Lumini E, Paolo D, Patanè C, Sparvoli F, Tucci M, Zampieri E. Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field. Int J Mol Sci 2021; 22:ijms22062887. [PMID: 33809189 PMCID: PMC7999214 DOI: 10.3390/ijms22062887] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/21/2022] Open
Abstract
Plant specialized metabolites (SMs) play an important role in the interaction with the environment and are part of the plant defense response. These natural products are volatile, semi-volatile and non-volatile compounds produced from common building blocks deriving from primary metabolic pathways and rapidly evolved to allow a better adaptation of plants to environmental cues. Specialized metabolites include terpenes, flavonoids, alkaloids, glucosinolates, tannins, resins, etc. that can be used as phytochemicals, food additives, flavoring agents and pharmaceutical compounds. This review will be focused on Mediterranean crop plants as a source of SMs, with a special attention on the strategies that can be used to modulate their production, including abiotic stresses, interaction with beneficial soil microorganisms and novel genetic approaches.
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Affiliation(s)
- Raffaella Balestrini
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
- Correspondence: ; Tel.: +39-01165-02927
| | - Cecilia Brunetti
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| | - Maria Cammareri
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Sofia Caretto
- CNR-Institute of Sciences of Food Production, Via Monteroni, 73100 Lecce, Italy; (S.C.); (G.G.)
| | - Valeria Cavallaro
- CNR-Institute of Bioeconomy (IBE), Via Paolo Gaifami, 18, 95126 Catania, Italy; (V.C.); (C.P.)
| | - Eleonora Cominelli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Monica De Palma
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Teresa Docimo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Giovanna Giovinazzo
- CNR-Institute of Sciences of Food Production, Via Monteroni, 73100 Lecce, Italy; (S.C.); (G.G.)
| | - Silvana Grandillo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Franca Locatelli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Erica Lumini
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| | - Dario Paolo
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Cristina Patanè
- CNR-Institute of Bioeconomy (IBE), Via Paolo Gaifami, 18, 95126 Catania, Italy; (V.C.); (C.P.)
| | - Francesca Sparvoli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Marina Tucci
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Elisa Zampieri
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
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Vinarao R, Proud C, Zhang X, Snell P, Fukai S, Mitchell J. Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System. RICE (NEW YORK, N.Y.) 2021; 14:28. [PMID: 33677700 PMCID: PMC7937586 DOI: 10.1186/s12284-021-00471-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/01/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109. RESULTS Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7-51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region. CONCLUSION Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.
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Affiliation(s)
- Ricky Vinarao
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Christopher Proud
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Xiaolu Zhang
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, 2703, Australia
| | - Shu Fukai
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Jaquie Mitchell
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia.
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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Oliveira GF, Nascimento ACC, Nascimento M, Sant'Anna IDC, Romero JV, Azevedo CF, Bhering LL, Moura ETC. Quantile regression in genomic selection for oligogenic traits in autogamous plants: A simulation study. PLoS One 2021; 16:e0243666. [PMID: 33400704 PMCID: PMC7785117 DOI: 10.1371/journal.pone.0243666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
This study assessed the efficiency of Genomic selection (GS) or genome-wide selection (GWS), based on Regularized Quantile Regression (RQR), in the selection of genotypes to breed autogamous plant populations with oligogenic traits. To this end, simulated data of an F2 population were used, with traits with different heritability levels (0.10, 0.20 and 0.40), controlled by four genes. The generations were advanced (up to F6) at two selection intensities (10% and 20%). The genomic genetic value was computed by RQR for different quantiles (0.10, 0.50 and 0.90), and by the traditional GWS methods, specifically RR-BLUP and BLASSO. A second objective was to find the statistical methodology that allows the fastest fixation of favorable alleles. In general, the results of the RQR model were better than or equal to those of traditional GWS methodologies, achieving the fixation of favorable alleles in most of the evaluated scenarios. At a heritability level of 0.40 and a selection intensity of 10%, RQR (0.50) was the only methodology that fixed the alleles quickly, i.e., in the fourth generation. Thus, it was concluded that the application of RQR in plant breeding, to simulated autogamous plant populations with oligogenic traits, could reduce time and consequently costs, due to the reduction of selfing generations to fix alleles in the evaluated scenarios.
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Affiliation(s)
| | | | - Moysés Nascimento
- Department of Statistics, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Juan Vicente Romero
- AGROSAVIA, The Colombian Agricultural Research Corporation, Mosquera, Colômbia
| | | | - Leonardo Lopes Bhering
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
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