1
|
Subedi M, Ghimire B, Bagwell JW, Buck JW, Mergoum M. Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities. Front Genet 2023; 13:1032601. [PMID: 36685944 PMCID: PMC9849398 DOI: 10.3389/fgene.2022.1032601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.
Collapse
Affiliation(s)
- Madhav Subedi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - John White Bagwell
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, United States,*Correspondence: Mohamed Mergoum,
| |
Collapse
|
2
|
Lotti C, Minervini AP, Delvento C, Losciale P, Gaeta L, Sánchez-Pérez R, Ricciardi L, Pavan S. Detection and distribution of two dominant alleles associated with the sweet kernel phenotype in almond cultivated germplasm. FRONTIERS IN PLANT SCIENCE 2023; 14:1171195. [PMID: 37123837 PMCID: PMC10145170 DOI: 10.3389/fpls.2023.1171195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Almond [Prunus dulcis Miller (D. A. Webb), syn. Prunus amygdalus L.)] is the major tree nut crop worldwide in terms of production and cultivated area. Almond domestication was enabled by the selection of individuals bearing sweet kernels, which do not accumulate high levels of the toxic cyanogenic glucoside amygdalin. Previously, we showed that the Sweet kernel (Sk) gene, controlling the kernel taste in almond, encodes a basic helix loop helix (bHLH) transcription factor regulating the amygdalin biosynthetic pathway. In addition, we characterized a dominant allele of this gene, further referred to as Sk-1, which originates from a C1036→T missense mutation and confers the sweet kernel phenotype. Here we provide evidence indicating that the allele further referred to as Sk-2, originally detected in the cultivar "Atocha" and arising from a T989→G missense mutation, is also dominantly inherited and confers the sweet kernel phenotype in almond cultivated germplasm. The use of single nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) for population structure and hierarchical clustering analyses indicated that Sk-2 occurs in a group of related genotypes, including the widespread cultivar "Texas", descending from the same ancestral population. KASP and dual label functional markers were developed for the accurate and high-throughput selection of the Sk-1 and Sk-2 alleles, and the genotyping of a panel of 134 almond cultivars. Overall, our results provide further insights on the understanding of the almond cultivation history. In addition, molecular marker assays and genotypic data presented in this study are expected to be of major interest for the conduction of almond breeding programs, which often need to select sweet kernel individuals in segregant populations.
Collapse
Affiliation(s)
- Concetta Lotti
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Foggia, Italy
| | - Anna Paola Minervini
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Chiara Delvento
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Losciale
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Liliana Gaeta
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment (CREA-AA), Bari, Italy
| | - Raquel Sánchez-Pérez
- Plant Breeding Department, Fruit Breeding Group, CEBAS-CSIC, Campus Universitario de Espinardo, Espinardo, Spain
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
- *Correspondence: Stefano Pavan,
| |
Collapse
|
3
|
Rashid M, Yousaf Z, Din A, Munawar M, Aftab A, Riaz N, Younas A, Alaraidh IA, Okla MK, AbdElgawad H. Assessment of Mineral Nutrient Efficiency in Genetically Diverse Spinach Accessions by Biochemical and Functional Marker Strategies. FRONTIERS IN PLANT SCIENCE 2022; 13:889604. [PMID: 35707614 PMCID: PMC9189916 DOI: 10.3389/fpls.2022.889604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/26/2022] [Indexed: 05/27/2023]
Abstract
Leafy vegetable crops are considered as a natural source of mineral nutrients that could decrease the risk factor of many growth issues in children and adults. Spinach is globally considered as the most desirable leafy crop, due to its taste and nutrient richness along with greater nitrate contents and better nitrogen use efficiency. To evaluate the mineral nutrient efficiency of this crop, thirty genetically diverse spinach accessions were analyzed through nutritional and functional marker strategies. The accession 163,310 from Pakistan was found to be rich in minerals (sodium, calcium, potassium, zinc, and manganese) and nitrates. However, the oxalate contents were lesser in the accessions that had greater quantity of nutrients. These represented a negative correlation between mineral availability and oxalate accumulation in the leaves. To study the relationship of oxalates and minerals in the accessions, a functional marker analysis was performed, based on the genes involved in oxalate metabolism and disease resistance in spinach. High level of genetic polymorphism was observed among the accessions represented with 115 polymorphic bands out of 130 bands. Heat map clustering represented the accessions from Asian countries (Pakistan, India, China, and Iran) as the most adaptable accessions to the local environment. The correlation between nutritional and genetic analysis also revealed the nutrient richness of these accessions along with good oxalate metabolism and disease resistance. Hence, these accessions could be considered as useful genotypes in future breeding programs.
Collapse
Affiliation(s)
- Madiha Rashid
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
- Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Zubaida Yousaf
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Ahmad Din
- National Institute of Food Science and Technology, Faculty of Food, Nutrition and Home Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muneeb Munawar
- Vegetable Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Arusa Aftab
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Nadia Riaz
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Ibrahim A. Alaraidh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K. Okla
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
4
|
The Butterfly Effect: Mild Soil Pollution with Heavy Metals Elicits Major Biological Consequences in Cobalt-Sensitized Broad Bean Model Plants. Antioxidants (Basel) 2022; 11:antiox11040793. [PMID: 35453478 PMCID: PMC9028058 DOI: 10.3390/antiox11040793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
Among the heavy metals (HMs), only cobalt induces a polymorphic response in Vicia faba plants, manifesting as chlorophyll morphoses and a ‘break-through’ effect resulting in the elevated accumulation of other HMs, which makes Co-pretreated broad bean plants an attractive model for investigating soil pollution by HMs. In this study, Co-sensitized V. faba plants were used to evaluate the long-term effect of residual industrial pollution by examining biochemical (H2O2, ascorbic acid, malondialdehyde, free proline, flavonoid, polyphenols, chlorophylls, carotenoids, superoxide dismutase) and molecular (conserved DNA-derived polymorphism and transcript-derived polymorphic fragments) markers after long-term exposure. HM-polluted soil induced a significantly higher frequency of chlorophyll morphoses and lower levels of nonenzymatic antioxidants in Co-pretreated V. faba plants. Both molecular markers effectively differentiated plants from polluted and control soils into distinct clusters, showing that HMs in mildly polluted soil are capable of inducing changes in DNA coding regions. These findings illustrate that strong background abiotic stressors (pretreatment with Co) can aid investigations of mild stressors (slight levels of soil pollution) by complementing each other in antioxidant content reduction and induction of DNA changes.
Collapse
|
5
|
Li R, Zheng W, Jiang M, Zhang H. A review of starch biosynthesis in cereal crops and its potential breeding applications in rice ( Oryza Sativa L.). PeerJ 2022; 9:e12678. [PMID: 35036154 PMCID: PMC8710062 DOI: 10.7717/peerj.12678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.
Collapse
Affiliation(s)
- Ruiqing Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.,College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wenyin Zheng
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Meng Jiang
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| |
Collapse
|
6
|
Liu X, Ding Q, Wang W, Pan Y, Tan C, Qiu Y, Chen Y, Li H, Li Y, Ye N, Xu N, Wu X, Ye R, Liu J, Ma C. Targeted Deletion of the First Intron of the Wx b Allele via CRISPR/Cas9 Significantly Increases Grain Amylose Content in Rice. RICE (NEW YORK, N.Y.) 2022; 15:1. [PMID: 34982277 PMCID: PMC8727654 DOI: 10.1186/s12284-021-00548-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 12/28/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND The rice Waxy (Wx) gene plays a major role in seed amylose synthesis and consequently controls grain amylose content. Wx gene expression is highly regulated at the post-transcriptional level. In particular, the GT/TT polymorphism at the 5'splicing site of its 1st intron greatly affects this intron's splicing efficiency and defines two predominant Wx alleles, Wxa and Wxb. Wxa rice often harbours intermediate to high amylose contents, whereas Wxb rice exhibits low to intermediate amylose contents. By deleting the Wx 1st intron using CRISPR/Cas9 technology, we generate a completely novel Wx allele and further investigate how intron removal affects Wx gene expression and rice grain amylose content. RESULTS CRISPR/Cas9-mediated targeted deletion of the Wx 1st intron was performed on 4 rice inbred lines: KY131 (Wxb), X32 (Wxb), X35 (Wxa) and X55 (Wxlv). Deletion of the 1st intron occurred in 8.6-11.8% of the primary transformants of these 4 inbred lines. Compared to wild-type plants, amylose content was significantly increased from 13.0% to approximately 24.0% in KY131 and X32 mutant lines, which both carried the Wxb allele. However, no significant difference in amylose content was observed between wild-type plants and X35 and X55 mutant lines, which carried the Wxa and Wxlv alleles, respectively. Wx gene expression analysis of wild-type plants and mutants yielded results that were highly consistent with amylose content results. KY131 and X32 mutants accumulated increased levels of steady mRNA transcripts compared with wild-type plants, whereas steady mRNA levels were not altered in X35 and X55 mutants compared with wild-type plants. Grain quality, including appearance quality and eating and cooking quality, which are tightly associated with amylose content, was also assessed in wild-type and mutant plants, and data were presented and analysed. CONCLUSIONS This study presents a novel and rapid strategy to increase amylose content in inbred rice carrying a Wxb allele. Our data strongly suggest that the 1st intron of the Wx gene regulates Wx gene expression mainly at the post-transcriptional level in rice. This finding is in contrast to a previous hypothesis suggesting that it influences Wx gene transcription. In addition, removal of the first intron generates a completely novel Wx allele. Further studies on this new Wx allele will provide invaluable insights into the regulation of Wx gene expression, which will help researchers engineer new Wx alleles to facilitate the breeding of rice cultivars with better eating and cooking quality.
Collapse
Affiliation(s)
- Xingdan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Ding
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Wenshu Wang
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yanling Pan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Chao Tan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yingbo Qiu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Ya Chen
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Hongjing Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yinlong Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Naizhong Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Nian Xu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Xiao Wu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Rongjian Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Jianfeng Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
| | - Chonglie Ma
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
| |
Collapse
|
7
|
Lee C, Chung CT, Hong WJ, Lee YS, Lee JH, Koh HJ, Jung KH. Transcriptional Changes in the Developing Rice Seeds Under Salt Stress Suggest Targets for Manipulating Seed Quality. FRONTIERS IN PLANT SCIENCE 2021; 12:748273. [PMID: 34819939 PMCID: PMC8606889 DOI: 10.3389/fpls.2021.748273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Global sea-level rise, the effect of climate change, poses a serious threat to rice production owing to saltwater intrusion and the accompanying increase in salt concentration. The reclaimed lands, comprising 22.1% of rice production in Korea, now face the crisis of global sea-level rise and a continuous increase in salt concentration. Here, we investigated the relationship between the decrease in seed quality and the transcriptional changes that occur in the developing rice seeds under salt stress. Compared to cultivation on normal land, the japonica rice cultivar, Samgwang, grown on reclaimed land showed a greatly increased accumulation of minerals, including sodium, magnesium, potassium, and sulfur, in seeds and a reduced yield, delayed heading, decreased thousand grain weight, and decreased palatability and amylose content. Samgwang showed phenotypical sensitivity to salt stress in the developing seeds. Using RNA-seq technology, we therefore carried out a comparative transcriptome analysis of the developing seeds grown on reclaimed and normal lands. In the biological process category, gene ontology enrichment analysis revealed that the upregulated genes were closely associated with the metabolism of biomolecules, including amino acids, carboxylic acid, lignin, trehalose, polysaccharide, and chitin, and to stress responses. MapMan analysis revealed the involvement of upregulated genes in the biosynthetic pathways of abscisic acid and melatonin and the relationship of trehalose, raffinose, and maltose with osmotic stress. Interestingly, many seed storage protein genes encoding glutelins and prolamins were upregulated in the developing seeds under salt stress, indicating the negative effect of the increase of storage proteins on palatability. Transcription factors upregulated in the developing seeds under salt stress included, in particular, bHLH, MYB, zinc finger, and heat shock factor, which could act as potential targets for the manipulation of seed quality under salt stress. Our study aims to develop a useful reference for elucidating the relationship between seed response mechanisms and decreased seed quality under salt stress, providing potential strategies for the improvement of seed quality under salt stress.
Collapse
Affiliation(s)
- Choonseok Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Chong-Tae Chung
- Crop Research Division, Chungcheongnam-do Agricultural Research and Extension Services, Yesan, South Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Yang-Seok Lee
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jong-Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Miryang, South Korea
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
8
|
Islam T, Reddy CK, Xu B. Pasting properties of rice marketed in Asian countries: a systematic study. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2021. [DOI: 10.1007/s11694-020-00741-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
9
|
Diaz Tatis P, López Carrascal CE. YUCA: PAN Y CARNE, UNA ALTERNATIVA POTENCIAL PARA HACER FRENTE AL HAMBRE OCULTA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n2.84569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Uno de los retos que encara la humanidad es asegurar la alimentación y la adecuada nutrición para los cerca de ocho billones de habitantes del planeta. Las raíces de yuca constituyen la cuarta fuente más importante de calorías para la población humana siendo uno de los pilares de la seguridad alimentaria. Las raíces de yuca no poseen atributos nutricionales adecuados. Aunque existen variedades con valores relativamente altos de estos compuestos, sus valores están lejos de los necesarios para asegurar los requerimientos mínimos de la población humana. Las hojas de yuca poseen valores altos de contenido proteico, minerales y vitaminas, por lo que representan una fuente nutricional alternativa. Sin embargo, el consumo de hojas de yuca en América Latina es escaso o nulo como consecuencia de los altos niveles de cianuro que poseen. En algunos países de África y Asia las hojas se consumen a través de diversas recetas que incluye su cocción, eliminando así una gran cantidad del contenido cianógeno. En esta revisión se presenta un panorama general de la importancia nutricional de la yuca, las diferentes estrategias de mejoramiento genético clásico y no convencional destinados a incrementar los contenidos nutricionales de raíces y la importancia de la explotación de la variabilidad intrínseca de la yuca como una fuente de variedades y genes que puedan contribuir a la implementación de estrategias encaminadas a desarrollar materiales con los requerimientos nutricionales adecuados. Finalmente, se presenta el potencial que tienen las hojas de yuca para ser empleadas dentro de programas complementarios destinados a mejorar la calidad nutricional de la población humana.
Collapse
|
10
|
Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
Collapse
Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
11
|
Erriu M, Cimino S, Cerniglia L. The Role of Family Relationships in Eating Disorders in Adolescents: A Narrative Review. Behav Sci (Basel) 2020; 10:E71. [PMID: 32252365 PMCID: PMC7226005 DOI: 10.3390/bs10040071] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/29/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Adolescents' eating disorders have been explored through various conceptual and empirical models. Only recently, scientific literature in this area has more specifically investigated the role of relationships, with particular attention to family functioning. Objective: This paper reviews family relationships aspects of eating disorders in adolescence. Methods: A narrative literature review of relational issues in adolescents' eating disorders was performed. Results: Empirical evidence of family relationships in adolescents' eating disorders confirms the relevance of relational aspects in the development and maintenance of the pathology. In particular, the contribution of the relational-systemic approach is wide, suggesting the need to refer to the family context for a better understanding of adolescents' sufferance. Additionally, the empirical contributions from the conceptual model of Developmental Psychopathology, highlighting the importance of risk and protection factors in family relationships, provides knowledge about the phenomenon of adolescents' eating disorders in terms of complexity. Conclusions: An integrated relational model aimed to explore adolescents' eating disorders is worthy of investigation to accomplish specific program of intervention.
Collapse
Affiliation(s)
- Michela Erriu
- Psychology and Medicine Faculty, Department of Dynamic and Clinical Psychology, Sapienza University of Rome, 00185 Rome, Italy; (M.E.); (S.C.)
| | - Silvia Cimino
- Psychology and Medicine Faculty, Department of Dynamic and Clinical Psychology, Sapienza University of Rome, 00185 Rome, Italy; (M.E.); (S.C.)
| | - Luca Cerniglia
- Psychology Faculty, Department of Psychology, International Telematic University Uninettuno, 00186 Rome, Italy
| |
Collapse
|
12
|
Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Muhammad I, Ubi BE, Nwokwu G. Genetic analysis of microsatellites associated with resistance against bacterial leaf blight and blast diseases of rice ( Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1809520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Isma’ila Muhammad
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - Gilbert Nwokwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| |
Collapse
|
13
|
Park SG, Park HS, Baek MK, Jeong JM, Cho YC, Lee GM, Lee CM, Suh JP, Kim CS, Kim SM. Improving the Glossiness of Cooked Rice, an Important Component of Visual Rice Grain Quality. RICE (NEW YORK, N.Y.) 2019; 12:87. [PMID: 31776807 PMCID: PMC6881499 DOI: 10.1186/s12284-019-0348-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/06/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rice is one of the few cereals consumed as a whole grain, and therefore the appearance of the final milled product, both before and after cooking, strongly influences the consumer's perception of product quality. Matching consumer preference for rice grain quality is a key component of rice variety development programs, as the quality drives demand, which in turn drives variety adoption, market price, and profitability. The quality of cooked rice is normally evaluated indirectly, through measurement of key elements driving quality as well as more directly by sensory evaluation, but remains a complex trait conditioned by the genetic complexity of factors driving quality, changes wrought by environment, and the complexity of consumer preferences. RESULT In this study, we evaluated 17 traits, including the taste value obtained by glossiness of cooked rice (TV), to explain rice eating quality by statistical methods and identified QTLs associated with TV. To explain the correlation among traits, exploratory factor analysis was performed for 2 years. The overall eating quality (OE) was correlated with TV and protein content loading at the same factor (PA1) in 2017, and there was a relationship between the OE (PA1) and the TV (PA2) in 2018 (PA1:PA2, r = 0.3). In QTL analysis using 174 RILs, three QTLs for TV derived from Wandoaengmi6 were detected on chromosomes 4, 6, and 9. The QTL qTV9 delimited within Id9007180 and 9,851,330 on chromosome 9 was detected in both years, explaining approximately 17% of the variation, on average. Through the use of fine mapping, qTV9 was delimited to an approximately 34-Kbp segment flanked by the DNA markers CTV9_9 and CTV9_13, and nine ORFs were listed in the target region as candidate genes associated with TV. In the evaluation of qTV9's effect on OE, the lines with qTV9 showed a significant increase in correlation coefficiency compared to the negative lines. These data will apply to functional analysis on the glossiness and the MAS breeding program to improve the eating quality of japonica as a donor line. CONCLUSION In this paper we report a number of QTL associated with changes in glossiness of cooked rice, and these may have utility in the development of MAS in breeding programs with a specific focus on cooked grain quality.
Collapse
Affiliation(s)
- Seul-Gi Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jong-Min Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Young-Chan Cho
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Gun-Mi Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jung-Pil Suh
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Choon-Song Kim
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Suk-Man Kim
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| |
Collapse
|
14
|
Mahender A, Ali J, Prahalada GD, Sevilla MAL, Balachiranjeevi CH, Md J, Maqsood U, Li Z. Genetic dissection of developmental responses of agro-morphological traits under different doses of nutrient fertilizers using high-density SNP markers. PLoS One 2019; 14:e0220066. [PMID: 31335882 PMCID: PMC6650078 DOI: 10.1371/journal.pone.0220066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The production and productivity of rice (Oryza sativa L.) are primarily influenced by the application of the critical nutrients nitrogen (N), phosphorus (P), and potassium (K). However, excessive application of these fertilizers is detrimental to the environment and increases the cost of production. Hence, there is a need to develop varieties that simultaneously increase yields under both optimal and suboptimal rates of fertilizer application by maximizing nutrient use efficiency (NuUE). To unravel the hidden genetic variation and understand the molecular and physiological mechanisms of NuUE, three different mapping populations (MPs; BC1F5) derived from three donors (Haoannong, Cheng-Hui 448, and Zhong 413) and recipient Weed Tolerant Rice 1 were developed. A total of three favorable agronomic traits (FATs) were considered as the measure of NuUE. Analysis of variance and descriptive statistics indicated the existence of genetic variation for NuUE and quantitative inheritance of FATs. The genotypic data from single-nucleotide polymorphism (SNP) markers from Tunable Genotyping-By-Sequencing (tGBS) and phenotypic values were used for locating the genomic regions conferring NuUE. A total of 19 quantitative trait loci (QTLs) were detected, out of which 11 QTLs were putative on eight chromosomes, which individually explained 17.02% to 34.85% of the phenotypic variation. Notably, qLC-II_1 and qLC-II_11 detected at zero fertilizer application showed higher performance for LC under zero percentage of NPK fertilizer. The remarkable findings of the present study are that the detected QTLs were associated in building tolerance to low/no nutrient application and six candidate genes on chromosomes 2 and 5 within these putative QTLs were found associated with low nutrient tolerance and related to several physiological and metabolic pathways involved in abiotic stress tolerance. The identified superior introgressed lines (ILs) and trait-associated genetic regions can be effectively used in marker-assisted selection (MAS) for NuUE breeding programs.
Collapse
Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
- * E-mail:
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Ma. Anna Lynn Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - C. H. Balachiranjeevi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jamaloddin Md
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan
| | - Zhikang Li
- Chinese Academy of Agricultural Sciences, Haidian District, P.R. China
| |
Collapse
|
15
|
Wambugu PW, Ndjiondjop MN, Henry RJ. Role of genomics in promoting the utilization of plant genetic resources in genebanks. Brief Funct Genomics 2019; 17:198-206. [PMID: 29688255 PMCID: PMC5967547 DOI: 10.1093/bfgp/ely014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended.
Collapse
Affiliation(s)
- Peterson W Wambugu
- Corresponding author: Robert Henry, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia. Tel.: ±61733460551; Fax: ±61733460555; E-mail:
| | | | | |
Collapse
|
16
|
Fiaz S, Ahmad S, Noor MA, Wang X, Younas A, Riaz A, Riaz A, Ali F. Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities. Int J Mol Sci 2019; 20:E888. [PMID: 30791357 PMCID: PMC6412304 DOI: 10.3390/ijms20040888] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/07/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023] Open
Abstract
Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.
Collapse
Affiliation(s)
- Sajid Fiaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing 100081, China.
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore 54000, Pakistan.
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Fahad Ali
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| |
Collapse
|
17
|
Descalsota-Empleo GI, Noraziyah AAS, Navea IP, Chung C, Dwiyanti MS, Labios RJD, Ikmal AM, Juanillas VM, Inabangan-Asilo MA, Amparado A, Reinke R, Cruz CMV, Chin JH, Swamy BPM. Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice. Genes (Basel) 2019; 10:E30. [PMID: 30626141 PMCID: PMC6356647 DOI: 10.3390/genes10010030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/16/2022] Open
Abstract
Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.
Collapse
Affiliation(s)
- Gwen Iris Descalsota-Empleo
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- University of the Southern Mindanao, Kabacan, Cotabato 9407, Philippines.
| | | | - Ian Paul Navea
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- Nousbo Corp. #4-107, 89 Seohoro, Gwonsun, Suwon 16614, Gyeonggi, Korea.
| | - Chongtae Chung
- Chungcheongnam-do Agricultural Research and Extension Services, 167, Chusa-ro, Shinam-myeon, Yesan-gun 32418, Chungcheongnam-do, Korea.
| | - Maria Stefanie Dwiyanti
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- Applied Plant Genome Laboratory, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.
| | | | - Asmuni Mohd Ikmal
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | | | | | - Amery Amparado
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
| | - Russell Reinke
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
| | | | - Joong Hyoun Chin
- Department of Integrative Bio-Industrial Engineering, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea.
| | | |
Collapse
|
18
|
Butardo VM, Sreenivasulu N, Juliano BO. Improving Rice Grain Quality: State-of-the-Art and Future Prospects. Methods Mol Biol 2019; 1892:19-55. [PMID: 30397798 DOI: 10.1007/978-1-4939-8914-0_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rice grain quality encompasses complex interrelated traits that cover biochemical composition, cooking, eating, nutritional, and sensory properties. Because rice endosperm is composed mainly of starch, rice grain quality is traditionally defined by characterizing starch structure and composition, which is then subsequently correlated with functional properties of the grain. The current proxy tests routinely used to describe rice grain quality preferences are rather limited to the estimation of apparent amylose content, gelatinization temperature, and gel consistency. Additional tests that characterize starch property, viscoelasticity, grain texture, and aroma are also employed in more advanced laboratories. However, these tests are not routinely applied in breeding programs to distinguish cooking quality classes to reflect evolving consumer preference and market demand. As consumer preferences in Asia and all over the world are diverse due to varied demographics and culture, defining uniform attributes to capture regional grain quality preferences becomes more challenging. Hence, novel and innovative proxy tests are needed to characterize rice grain quality to meet the demand for consumer preferences of commercially-released cultivars. In this chapter, the current methods employed in rice grain quality monitoring are succinctly reviewed. Future prospects for improvement are identified, introducing cutting edge technologies that can facilitate high-throughput screening of rice diversity panels and breeding lines. Aside from addressing the requirements for quality improvement in the traditional inbred rice breeding programs, we also tackled the need to enhance grain quality in the hybrid rice sector.
Collapse
Affiliation(s)
- Vito M Butardo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Nese Sreenivasulu
- International Rice Research Institute, Los Baños, Laguna, Philippines.
| | | |
Collapse
|
19
|
Li Q, Liu X, Zhang C, Jiang L, Jiang M, Zhong M, Fan X, Gu M, Liu Q. Rice Soluble Starch Synthase I: Allelic Variation, Expression, Function, and Interaction With Waxy. FRONTIERS IN PLANT SCIENCE 2018; 9:1591. [PMID: 30483281 PMCID: PMC6243471 DOI: 10.3389/fpls.2018.01591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/15/2018] [Indexed: 05/07/2023]
Abstract
Starch, which is composed of amylose and amylopectin, is the key determinant of rice quality. Amylose is regulated by the Waxy (Wx) gene, whereas amylopectin is coordinated by various enzymes including eight soluble starch synthases (SSSs), of which SSSI accounts for ∼70% of the total SSS activity in cereal endosperm. Although great progress has been made in understanding SSSI gene expression and function, allelic variation and its effects on gene expression, rice physicochemical properties and qualities, and interactions with the Wx gene remain unclear. Herein, SSSI nucleotide polymorphisms were analyzed in 165 rice varieties using five distinct molecular markers, three of which reside in an SSSI promoter and might account for a higher expression of the SSSIi allele in indica ssp. than of the SSSIj allele in japonica ssp. The results of SSSI promoter-Beta-Glucuronidase (β-GUS) analysis were consistent with the expression results. Moreover, analysis of near isogenic lines (NILs) in the Nipponbare (Nip) background showed that Nip (SSSIi ) and Nip (SSSIj ) differed in their thermal properties, gel consistency (GC), and granule crystal structure. Knockdown of SSSI expression using the SSSI-RNA interference (RNAi) construct in both japonica and indica backgrounds caused consistent changes in most tested physicochemical characteristics except GC. Moreover, taste value analysis (TVA) showed that introduction of the SSSI allele in indica or knockdown of SSSI expression in japonica cultivars significantly reduced the comprehensive taste value, which was consistent with the superior taste of japonica against indica. Furthermore, to test the potential interaction between SSSI and different Wx alleles, three NILs within the Wx locus were generated in the indica cv. Longtefu (LTF) background, which were designated as LTF (Wxa ), LTF (Wxb ), and LTF (wx). The SSSI-RNAi construct was also introduced into these three NILs, and physiochemical analysis confirmed that the knockdown of SSSI significantly increased the rice apparent amylose content (AAC) only in the Wxa and Wxb background and caused different changes in GC in the NILs. Therefore, the effect of SSSI variation on rice quality also depends on its crosstalk with other factors, especially the Wx gene. These findings provide fundamental knowledge for future breeding of rice with premium eating and cooking qualities.
Collapse
Affiliation(s)
- Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xinyan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Li Jiang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Meiyan Jiang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Min Zhong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Qiaoquan Liu,
| |
Collapse
|
20
|
Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N, Özkan H, Chung G, Baloch FS. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1400401] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, P. R. China
| | - Yıldız Doğan
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Gonul Comertpay
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Mehtap Yıldız
- Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yıl University, Van, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Fiaz Ahmad
- Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Punjab, Pakistan
| | - Ahmad Alsaleh
- Molecular Genetics Laboratory, Science and Technology Application and Research Center, Bozok University, Yozgat, Turkey
| | - Nitin Labhane
- Department of Botany, Bhavan's College, University of Mumbai, Mumbai, India
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| |
Collapse
|
21
|
Fu YB, Yang MH, Zeng F, Biligetu B. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:1182. [PMID: 28729875 PMCID: PMC5498511 DOI: 10.3389/fpls.2017.01182] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/20/2017] [Indexed: 05/09/2023]
Abstract
Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SaskatoonSK, Canada
- *Correspondence: Yong-Bi Fu,
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SaskatoonSK, Canada
- College of Forestry, Central South University of Forestry and TechnologyChangsha, China
| | - Fangqin Zeng
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SaskatoonSK, Canada
| | - Bill Biligetu
- Department of Plant Sciences, University of Saskatchewan, SaskatoonSK, Canada
| |
Collapse
|