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Khound R, Rajput SG, Schnable JC, Vetriventhan M, Santra DK. Genome-wide association study reveals marker-trait associations for major agronomic traits in proso millet (Panicum miliaceum L.). PLANTA 2024; 260:44. [PMID: 38963439 DOI: 10.1007/s00425-024-04465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
MAIN CONCLUSION The pilot-scale genome-wide association study in the US proso millet identified twenty marker-trait associations for five morpho-agronomic traits identifying genomic regions for future studies (e.g. molecular breeding and map-based cloning). Proso millet (Panicum miliaceum L.) is an ancient grain recognized for its excellent water-use efficiency and short growing season. It is an indispensable part of the winter wheat-based dryland cropping system in the High Plains of the USA. Its grains are endowed with high nutritional and health-promoting properties, making it increasingly popular in the global market for healthy grains. There is a dearth of genomic resources in proso millet for developing molecular tools to complement conventional breeding for developing high-yielding varieties. Genome-wide association study (GWAS) is a widely used method to dissect the genetics of complex traits. In this pilot study of the first-ever GWAS in the US proso millet, 71 globally diverse genotypes of 109 the US proso millet core collection were evaluated for five major morpho-agronomic traits at two locations in western Nebraska, and GWAS was conducted to identify single nucleotide polymorphisms (SNPs) associated with these traits. Analysis of variance showed that there was a significant difference among the genotypes, and all five traits were also found to be highly correlated with each other. Sequence reads from genotyping-by-sequencing (GBS) were used to identify 11,147 high-quality bi-allelic SNPs. Population structure analysis with those SNPs showed stratification within the core collection. The GWAS identified twenty marker-trait associations (MTAs) for the five traits. Twenty-nine putative candidate genes associated with the five traits were also identified. These genomic regions can be used to develop genetic markers for marker-assisted selection in proso millet breeding.
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Affiliation(s)
- Rituraj Khound
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Santosh G Rajput
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Dryland Genetics Inc, Ames, IA, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Mani Vetriventhan
- Genebank, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Dipak K Santra
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Wang XH, Lee MC, Choi YM, Kim SH, Han S, Desta KT, Yoon HM, Lee YJ, Oh MA, Yi JY, Shin MJ. Phylogeography and Antioxidant Activity of Proso Millet ( Panicum miliaceum L.). PLANTS 2021; 10:plants10102112. [PMID: 34685921 PMCID: PMC8537217 DOI: 10.3390/plants10102112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022]
Abstract
Proso millet (Panicum miliaceum L.) or broomcorn millet is among the most important food crops to be domesticated by humans; it is widely distributed in America, Europe, and Asia. In this study, we genotyped 578 accessions of P. miliaceum using 37 single-sequence repeat (SSR) markers, to study the genetic diversity and population structure of each accession. We also investigated total phenolic content (TPC) and superoxide dismutase (SOD) activity and performed association analysis using SSR markers. The results showed that genetic diversity and genetic distance were related to geographic location and the fixation index (Fst). Population structure analysis divided the population into three subpopulations. Based on 3 subpopulations, the population is divided into six clusters in consideration of geographical distribution characteristics and agronomic traits. Based on the genetic diversity, population structure, pairwise Fst, and gene flow analyses, we described the topological structure of the six proso millet subpopulations, and the geographic distribution and migration of each cluster. Comparison of the published cluster (cluster 1) with unique germplasms in Japan and South Korea suggested Turkey as a possible secondary center of origin and domestication (cluster 3) for the cluster. We also discovered a cluster domesticated in Nepal (cluster 6) that is adapted to high-latitude and high-altitude cultivation conditions. Differences in phenotypic characteristics, such as TPC, were observed between the clusters. The association analysis showed that TPC was associated with SSR-31, which explained 7.1% of the total variance, respectively. The development of markers associated with TPC and SOD will provide breeders with new tools to improve the quality of proso millet through marker-assisted selection.
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Affiliation(s)
- Xiao-Han Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Myung-Chul Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Yu-Mi Choi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Seahee Han
- Honam National Institute of Biological Resources, Mokpo 58762, Korea;
| | - Kebede Taye Desta
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
- Department of Applied Chemistry, Adama Science and Technology University, Adama 1888, Ethiopia
| | - Hye-Myeong Yoon
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Mi-Ae Oh
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Jung-Yoon Yi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (X.-H.W.); (M.-C.L.); (Y.-M.C.); (S.-H.K.); (K.T.D.); (H.-M.Y.); (Y.-J.L.); (M.-A.O.); (J.-Y.Y.)
- Correspondence: ; Tel.: +82-63-238-4891
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Rajasekaran R, Francis N. Genetic and genomic resources for improving proso millet (Panicum miliaceum L.): a potential crop for food and nutritional security. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00331-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Renganathan VG, Vanniarajan C, Karthikeyan A, Ramalingam J. Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction. Front Genet 2020; 11:500. [PMID: 32655612 PMCID: PMC7325689 DOI: 10.3389/fgene.2020.00500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023] Open
Abstract
Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Jegadeesan Ramalingam
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
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Zheng M, Xiao Y, Yang S, Liu H, Liu M, Yaqoob S, Xu X, Liu J. Effects of heat-moisture, autoclaving, and microwave treatments on physicochemical properties of proso millet starch. Food Sci Nutr 2020; 8:735-743. [PMID: 32148783 PMCID: PMC7020272 DOI: 10.1002/fsn3.1295] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022] Open
Abstract
Proso millet starch was modified by heat-moisture treatment (HMT), autoclaving treatment (AT), and microwave treatment (MT). The effects of these treatments on the starch physicochemical, structural, and molecular properties were investigated. The amylose and resistant starch contents were increased by AT and MT, but only slightly by HMT. HMT and AT significantly increased the water-holding capacity, to 172.66% and 191.63%, respectively. X-ray diffractometry showed that the relative crystallinity of the HMT sample decreased by 20.88%, and the crystalline peaks disappeared from the AT and MT sample patterns. The thermal treatments decreased the proso millet starch molecular weight to 1.769 × 106, 7.886 × 105, and 3.411 × 104 g/mol, respectively. The thermal enthalpy decreased significantly in HMT. Modification significantly changed the pasting profiles of the native proso millet starch, and the peak viscosity, setback, and breakdown values decreased. These results clarify the mechanism of starch changes caused by thermal treatment.
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Affiliation(s)
- Ming‐zhu Zheng
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
| | - Yu Xiao
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
| | - Shuang Yang
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
| | - Hui‐min Liu
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
- College of Life ScienceJilin Agricultural UniversityChangchunJilinChina
| | - Mei‐hong Liu
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
| | - Sanabil Yaqoob
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
| | - Xiu‐ying Xu
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
| | - Jing‐sheng Liu
- College of Food Science and EngineeringJilin Agricultural UniversityChangchunJilinChina
- National Engineering Laboratory for Wheat and Corn Deep ProcessingChangchunJilinChina
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Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H. The genome of broomcorn millet. Nat Commun 2019; 10:436. [PMID: 30683860 PMCID: PMC6347628 DOI: 10.1038/s41467-019-08409-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.
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Affiliation(s)
- Changsong Zou
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, 475001, Kaifeng, Henan, China
| | - Leiting Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Delin Li
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
| | - Qiming Tang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Lihong Xiao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | | | - Ping Deng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Ru Huang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Meiling Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Yidan Sun
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Jiamin Hu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3650, USA
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Feng Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Hui Zhang
- Key Laboratory of Plant Stress Research, Shandong Normal University, No. 88 Wenhua East Rd, Jinan, 250014, Shandong, China
| | - Baili Feng
- School of Agronomy, Northwest Agriculture & Forestry University, 3 Weihui Rd, 712100, Yangling, China
| | - Xinguang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, 200032, Shanghai, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - James C Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
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Li W, Gao J, Saleh ASM, Tian X, Wang P, Jiang H, Zhang G. The Modifications in Physicochemical and Functional Properties of Proso Millet Starch after Ultra-High Pressure (UHP) Process. STARCH-STARKE 2018. [DOI: 10.1002/star.201700235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wenhao Li
- College of Food Science and Engineering; Northwest A&F University; Yangling 712100 China
| | - Jiaxing Gao
- College of Food Science and Engineering; Northwest A&F University; Yangling 712100 China
| | - Ahmed S. M. Saleh
- Department of Food Science and Technology; Faculty of Agriculture; Assiut University; Assiut 71526 Egypt
| | - Xiaolin Tian
- College of Food Science and Engineering; Northwest A&F University; Yangling 712100 China
| | - Peng Wang
- College of Food Science and Engineering; Northwest A&F University; Yangling 712100 China
| | - Hao Jiang
- College of Food Science and Engineering; Northwest A&F University; Yangling 712100 China
| | - Guoquan Zhang
- College of Food Science and Engineering; Northwest A&F University; Yangling 712100 China
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Nazari B, Mohammadifar MA, Shojaee-Aliabadi S, Feizollahi E, Mirmoghtadaie L. Effect of ultrasound treatments on functional properties and structure of millet protein concentrate. ULTRASONICS SONOCHEMISTRY 2018; 41:382-388. [PMID: 29137765 DOI: 10.1016/j.ultsonch.2017.10.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 08/02/2017] [Accepted: 10/03/2017] [Indexed: 05/25/2023]
Abstract
In this study, the effect of high power ultrasound (US) probe in varying intensities and times (18.4, 29.58, and 73.95 W/cm2 for 5, 12.5 and 20 min respectively) on functional properties of millet protein concentrate (MPC) was investigated, and also the structural properties of best modified treatment were evaluated by FTIR, DSC, Zeta potential and SDS-PAGE techniques. The results showed the solubility in all US treated MPC was significantly (p < .05) higher than those of the native MPC. Foaming capacity of native MPC (271.03 ± 4.51 ml) was reduced after US treatments at low intensities (82.37 ± 5.51 ml), but increased upon US treatments at high intensities (749.7 ± 2 ml). In addition, EAI and ES increased after US treatments. One of the best US treatments that can improve the functional properties of MPC was 73.95 W/cm2 for 12.5 min that resulted in reduction of molecular weight and increase nearly 36% in the negative surface charge that was confirmed by SDS-page and Zeta potential results, respectively.
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Affiliation(s)
- Bahman Nazari
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Mohammadifar
- Food Production Engineering, DTU Food, Technical University Of Denmark, Søltofts Plads227, Dk-2800 Lyngby, Denmark
| | - Saeedeh Shojaee-Aliabadi
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Feizollahi
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Mirmoghtadaie
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Tyl C, Marti A, Hayek J, Anderson J, Ismail BP. Effect of growing location and variety on nutritional and functional properties of proso millet (Panicum miliaceum) grown as a double crop. Cereal Chem 2018. [DOI: 10.1002/cche.10028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Catrin Tyl
- Department of Food Science and Nutrition; University of Minnesota; Saint Paul MN USA
| | - Alessandra Marti
- Department of Food Science and Nutrition; University of Minnesota; Saint Paul MN USA
- Department of Food, Environmental and Nutritional Sciences; Università degli Studi di Milano; Milan Italy
| | - Jenny Hayek
- Department of Food Science and Nutrition; University of Minnesota; Saint Paul MN USA
| | - James Anderson
- Department of Plant Agronomy and Plant Genetics; University of Minnesota; Saint Paul MN USA
| | - Baraem P. Ismail
- Department of Food Science and Nutrition; University of Minnesota; Saint Paul MN USA
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Hou S, Sun Z, Li Y, Wang Y, Ling H, Xing G, Han Y, Li H. Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet ( Panicum miliaceum; Poaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600137. [PMID: 28791202 PMCID: PMC5546162 DOI: 10.3732/apps.1600137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 05/02/2017] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Proso millet (Panicum miliaceum; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers. METHODS Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated. RESULTS In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups. DISCUSSION A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future.
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Affiliation(s)
- Siyu Hou
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taigu, Shanxi 030801, People’s Republic of China
| | - Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Yaoshen Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Yijie Wang
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Hubin Ling
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Guofang Xing
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taigu, Shanxi 030801, People’s Republic of China
| | - Yuanhuai Han
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Institute of Crop Genetic Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi 030031, People’s Republic of China
| | - Hongying Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
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Habiyaremye C, Matanguihan JB, D’Alpoim Guedes J, Ganjyal GM, Whiteman MR, Kidwell KK, Murphy KM. Proso Millet ( Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review. FRONTIERS IN PLANT SCIENCE 2017; 7:1961. [PMID: 28119699 PMCID: PMC5220228 DOI: 10.3389/fpls.2016.01961] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/12/2016] [Indexed: 05/25/2023]
Abstract
Proso millet (Panicum miliaceum L.) is a warm season grass with a growing season of 60-100 days. It is a highly nutritious cereal grain used for human consumption, bird seed, and/or ethanol production. Unique characteristics, such as drought and heat tolerance, make proso millet a promising alternative cash crop for the Pacific Northwest (PNW) region of the United States. Development of proso millet varieties adapted to dryland farming regions of the PNW could give growers a much-needed option for diversifying their predominantly wheat-based cropping systems. In this review, the agronomic characteristics of proso millet are discussed, with emphasis on growth habits and environmental requirements, place in prevailing crop rotations in the PNW, and nutritional and health benefits. The genetics of proso millet and the genomic resources available for breeding adapted varieties are also discussed. Last, challenges and opportunities of proso millet cultivation in the PNW are explored, including the potential for entering novel and regional markets.
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Affiliation(s)
- Cedric Habiyaremye
- Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State UniversityPullman, WA, USA
| | - Janet B. Matanguihan
- Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State UniversityPullman, WA, USA
| | | | - Girish M. Ganjyal
- Food Processing Lab, School of Food Science, College of Agricultural, Human, and Natural Resource Sciences, Washington State UniversityPullman, WA, USA
| | - Michael R. Whiteman
- International Programs, International Research and Agricultural Development, Washington State UniversityPullman, WA, USA
| | - Kimberlee K. Kidwell
- College of Agricultural, Consumer, and Environmental Sciences, University of IllinoisUrbana, IL, USA
| | - Kevin M. Murphy
- Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State UniversityPullman, WA, USA
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Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers. Int J Mol Sci 2016; 17:370. [PMID: 26985894 PMCID: PMC4813230 DOI: 10.3390/ijms17030370] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/02/2016] [Accepted: 03/08/2016] [Indexed: 11/24/2022] Open
Abstract
Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet.
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Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, Al-Dhabi NA, Ignacimuthu S. Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers. SPRINGERPLUS 2016; 5:120. [PMID: 26900542 PMCID: PMC4749518 DOI: 10.1186/s40064-015-1626-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/16/2015] [Indexed: 12/01/2022]
Abstract
We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60–70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard’s similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard’s similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on their geographic regions.
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Affiliation(s)
- M Ramakrishnan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India
| | - S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Faculty of Biological Sciences, Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT UK
| | - V Duraipandiyan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| | - N A Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| | - S Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Visiting Professor Program, Deanship of Scientific Research, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
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15
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Gong M, Li X, Xiong L, Sun Q. Retrogradation property of starch nanoparticles prepared by pullulanase and recrystallization. STARCH-STARKE 2015. [DOI: 10.1002/star.201500115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Min Gong
- School of Food Science and Engineering; Qingdao Agricultural University; Qingdao P.R. China
| | - Xiaojing Li
- School of Food Science and Engineering; Qingdao Agricultural University; Qingdao P.R. China
| | - Liu Xiong
- School of Food Science and Engineering; Qingdao Agricultural University; Qingdao P.R. China
| | - Qingjie Sun
- School of Food Science and Engineering; Qingdao Agricultural University; Qingdao P.R. China
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16
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Goron TL, Raizada MN. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution. FRONTIERS IN PLANT SCIENCE 2015; 6:157. [PMID: 25852710 PMCID: PMC4371761 DOI: 10.3389/fpls.2015.00157] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 02/27/2015] [Indexed: 05/20/2023]
Abstract
Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.
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Affiliation(s)
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
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17
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Goron TL, Raizada MN. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 25852710 DOI: 10.3389/fpl.2015.00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.
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Affiliation(s)
- Travis L Goron
- Department of Plant Agriculture, University of Guelph Guelph, ON, Canada
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph Guelph, ON, Canada
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18
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Effect of retrogradation time on preparation and characterization of proso millet starch nanoparticles. Carbohydr Polym 2014; 111:133-8. [DOI: 10.1016/j.carbpol.2014.03.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 11/21/2022]
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19
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Effect of dry heat treatment on the physicochemical properties and structure of proso millet flour and starch. Carbohydr Polym 2014; 110:128-34. [PMID: 24906738 DOI: 10.1016/j.carbpol.2014.03.090] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/01/2014] [Accepted: 03/30/2014] [Indexed: 11/22/2022]
Abstract
Proso millet (Panicum miliaceum L.) flour and starch were heated in a dry state at 130°C for 2 or 4 h. The effects of dry heat treatment (DHT) on the pasting, morphological and structural properties of the samples were evaluated. Dry heat treatment had a more significant effect on the pasting viscosity of flour than starch; it increased the pasting viscosity of the flour while it only increased the final viscosity of the starch. After dry heating, the onset of gelatinization and the peak temperatures of the samples increased significantly while the endothermic enthalpy decreased. Scanning electron microscopy showed that the gel structure of the samples became more compact and the particles were plumper when compared with the native ones. Crystallinity of the samples decreased while the X-ray diffraction patterns remained the same after DHT.
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20
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Rajput SG, Plyler-Harveson T, Santra DK. Development and Characterization of SSR Markers in Proso Millet Based on Switchgrass Genomics. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.51023] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Hunt HV, Moots HM, Graybosch RA, Jones H, Parker M, Romanova O, Jones MK, Howe CJ, Trafford K. Waxy phenotype evolution in the allotetraploid cereal broomcorn millet: mutations at the GBSSI locus in their functional and phylogenetic context. Mol Biol Evol 2012; 30:109-22. [PMID: 22936718 PMCID: PMC3533377 DOI: 10.1093/molbev/mss209] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Waxy mutants, in which endosperm starch contains ~100% amylopectin rather than the wild-type composition of ~70% amylopectin and ~30% amylose, occur in many domesticated cereals. The cultivation of waxy varieties is concentrated in east Asia, where there is a culinary preference for glutinous-textured foods that may have developed from ancient food processing traditions. The waxy phenotype results from mutations in the GBSSI gene, which catalyzes amylose synthesis. Broomcorn or proso millet (Panicum miliaceum L.) is one of the world's oldest cultivated cereals, which spread across Eurasia early in prehistory. Recent phylogeographic analysis has shown strong genetic structuring that likely reflects ancient expansion patterns. Broomcorn millet is highly unusual in being an allotetraploid cereal with fully waxy varieties. Previous work characterized two homeologous GBSSI loci, with multiple alleles at each, but could not determine whether both loci contributed to GBSSI function. We first tested the relative contribution of the two GBSSI loci to amylose synthesis and second tested the association between GBSSI alleles and phylogeographic structure inferred from simple sequence repeats (SSRs). We evaluated the phenotype of all known GBSSI genotypes in broomcorn millet by assaying starch composition and protein function. The results showed that the GBSSI-S locus is the major locus controlling endosperm amylose content, and the GBSSI-L locus has strongly reduced synthesis capacity. We genotyped 178 individuals from landraces from across Eurasia for the 2 GBSSI and 16 SSR loci and analyzed phylogeographic structuring and the geographic and phylogenetic distribution of GBSSI alleles. We found that GBSSI alleles have distinct spatial distributions and strong associations with particular genetic clusters defined by SSRs. The combination of alleles that results in a partially waxy phenotype does not exist in landrace populations. Our data suggest that broomcorn millet is a system in the process of becoming diploidized for the GBSSI locus responsible for grain amylose. Mutant alleles show some exchange between genetic groups, which was favored by selection for the waxy phenotype in particular regions. Partially waxy phenotypes were probably selected against-this unexpected finding shows that better understanding is needed of the human biology of this phenomenon that distinguishes cereal use in eastern and western cultures.
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Affiliation(s)
- Harriet V Hunt
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom.
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22
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Lu FH, Kwon SW, Yoon MY, Kim KT, Cho MC, Yoon MK, Park YJ. SNP marker integration and QTL analysis of 12 agronomic and morphological traits in F₈ RILs of pepper (Capsicum annuum L.). Mol Cells 2012; 34:25-34. [PMID: 22684870 PMCID: PMC3887781 DOI: 10.1007/s10059-012-0018-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 01/05/2023] Open
Abstract
Red pepper, Capsicum annuum L., has been attracting geneticists' and breeders' attention as one of the important agronomic crops. This study was to integrate 41 SNP markers newly developed from comparative transcriptomes into a previous linkage map, and map 12 agronomic and morphological traits into the integrated map. A total of 39 markers found precise position and were assigned to 13 linkage groups (LGs) as well as the unassigned LGe, leading to total 458 molecular markers present in this genetic map. Linkage mapping was supported by the physical mapping to tomato and potato genomes using BLAST retrieving, revealing at least two-thirds of the markers mapped to the corresponding LGs. A sum of 23 quantitative trait loci from 11 traits was detected using the composite interval mapping algorithm. A consistent interval between a035_1 and a170_1 on LG5 was detected as a main-effect locus among the resistance QTLs to Phytophthora capsici at high-, intermediate- and low-level tests, and interactions between the QTLs for high-level resistance test were found. Considering the epistatic effect, those QTLs could explain up to 98.25% of the phenotype variations of resistance. Moreover, 17 QTLs for another eight traits were found to locate on LG3, 4, and 12 mostly with varying phenotypic contribution. Furthermore, the locus for corolla color was mapped to LG10 as a marker. The integrated map and the QTLs identified would be helpful for current genetics research and crop breeding, especially in the Solanaceae family.
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Affiliation(s)
- Fu-Hao Lu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
| | - Soon-Wook Kwon
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
- Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-702,
Korea
| | - Min-Young Yoon
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
| | - Ki-Taek Kim
- The Foundation of Agricultural Technology Commercialization and Transfer, Suwon 441-100,
Korea
| | - Myeong-Cheoul Cho
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440,
Korea
| | - Moo-Kyung Yoon
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440,
Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
- Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-702,
Korea
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23
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EST-SSRs characterization and in-silico alignments with linkage map SSR loci in grape (Vitis L.) genome. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0121-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Hunt HV, Campana MG, Lawes MC, Park YJ, Bower MA, Howe CJ, Jones MK. Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia. Mol Ecol 2011; 20:4756-71. [PMID: 22004244 PMCID: PMC3258423 DOI: 10.1111/j.1365-294x.2011.05318.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/31/2011] [Accepted: 09/02/2011] [Indexed: 12/25/2022]
Abstract
Broomcorn millet (Panicum miliaceum L.) is one of the world's oldest cultivated cereals, with several lines of recent evidence indicating that it was grown in northern China from at least 10,000 cal bp. Additionally, a cluster of archaeobotanical records of P. miliaceum dated to at least 7000 cal bp exists in eastern Europe. These two centres of early records could either represent independent domestications or cross-continental movement of this cereal that would predate that of any other crop by some 2 millennia. Here, we analysed genetic diversity among 98 landrace accessions from across Eurasia using 16 microsatellite loci, to explore phylogeographic structure in the Old World range of this historically important crop. The major genetic split in the data divided the accessions into an eastern and a western grouping with an approximate boundary in northwestern China. A substantial number of accessions belonging to the 'western' genetic group were also found in northeastern China. Further resolution subdivided the western and eastern genepools into 2 and 4 clusters respectively, each showing clear geographic patterning. The genetic data are consistent with both the single and multiple domestication centre hypotheses and add specific detail to what these hypotheses would entail regarding the spread of broomcorn millet. Discrepancies exist between the predictions from the genetic data and the current archaeobotanical record, highlighting priorities for investigation into early farming in Central Asia.
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Affiliation(s)
- Harriet V Hunt
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK.
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