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Sedah P, Djedatin LG, Loko LYE, Gbemavo CDSJ, Orobiyi A, Toffa J, Tchakpa C, Ewedje EEBK, Sabot F. Agro-morphological and structural diversity of rice germplasm revealed by SSR markers in Benin Republic. Mol Biol Rep 2023; 50:10207-10217. [PMID: 37924445 DOI: 10.1007/s11033-023-08874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/02/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND In developing countries, rice is a staple food and cash crop for the people. In Benin Republic, paddy rice production has increased over time. Accordingly, local varieties were replaced by improved varieties, leading unfortunatley to a loss of the diversity of Beninese rice germplasm. METHODS AND RESULTS The investigation focused on the structure and genetic diversity of 72 rice accessions collected throughout 22 villages using 13 quantitative traits and 17 SSR markers. The descriptive analysis of the 13 quantitative parameters showed a significant difference among the accessions, with a grouping in three clusters. Group I (16.66% of samples) was composed of accessions with long, wide and thick grains alongside with four controls TOG5681, TOG5307, Azucena and Moroberekan. Group II (7% of samples) contained accessions with late vegetative cycle. Group III contained most of the accessions (76.39% of the samples), including accessions such as the CG14 and Nipponbare control lines, and almost all the improved varieties. The molecular analysis revealed a significant diversity (mean number of alleles: 4.47 with polymorphism information content of 0.633). Population structure based on molecular markers showed three primary populations with a mixture of phenotypic groupings at ΔK, K = 3. CONCLUSION This study showed that Beninese rice germplasm was divided into two structures: phenotypically similar cultivars but genotypically distinct (homonyms), and phenotypically different cultivars but genotypically similar (synonyms). Some local cultivars such Bagou19, Bagou20 and Koud44 can be used for large scale production due to their agronomics and molecular traits. The molecular structure obtained in this investigation might be used for future conservation and breeding programs.
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Affiliation(s)
- Paulin Sedah
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin.
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France.
| | - Lambert Gustave Djedatin
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Laura Yêyinou Estelle Loko
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Chalemagne Dossou Seblodo Judes Gbemavo
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Azize Orobiyi
- Institut National des Recherches Agricoles du Bénin (INRAB), Cotonou, 01 B P 884, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Joelle Toffa
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Cyrille Tchakpa
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Eben-Ezer Baba Kayodé Ewedje
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
| | - Francois Sabot
- DIADE unit, UM, CIRAD IRD, Centre IRD de Montpellier, 911 Agropolis BP 604501, Montpellier Cedex 5, F-34 394, France
- Jeune Equipe Associée à l'Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France
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Xia Q, Anwar U, Weijian Y, Yingshuai W, Hui L. Genetic characteristics of spouse selection based on short tandem repeats in DNA and lunula count on fingertip. Genes Environ 2023; 45:26. [PMID: 37864262 PMCID: PMC10588066 DOI: 10.1186/s41021-023-00281-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023] Open
Abstract
OBJECTIVE The aim of this study was to assess the correlation of spouse selection with short tandem repeats (STRs) in DNA and with the number of fingertip lunulae to investigate the role of heredity in spouse selection. METHODS We randomly selected a total of 286 couples (husband and wife) as a couple group while 200 paired subjects (a man randomly matched with a woman as a pair of subjects) were selected as a non-spouse group for DNA typing, and to investigate lunulae in spouse selection, a total of 554 couples were selected as a couple group and 500 pairs of subjects were selected as a control group. RESULTS A significant difference of STR matching number (a large value implies a higher genetic similarity) between spouse group and non-spouse group were observed (12.3 ± 2.7 vs. 11.8 ± 2.6; p < 0.05). A significant difference of the lunula matching number (difference of lunula counts between a paired subjects, a lower value implies a higher genetic similarity) between two groups were also observed for the lunula counts (1.55 ± 1.88 vs. 3.53 ± 2.40; p < 0.01). CONCLUSION Significant and unprecedented relationships were found between the couples and polymorphic STRs, and between spouse selection and lunula counts. Polymorphic STRs and fingertip lunulae counts provide an initial insight into the potentially important contributions that genetic characteristics may play a key role in spouse selection.
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Affiliation(s)
- Qi Xia
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Ullah Anwar
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Yu Weijian
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Wang Yingshuai
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China.
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Halim AABA, Rafii MY, Osman MB, Chukwu SC, Oladosu Y. Physicochemical Properties and Tissue Structure of High Kernel Elongation Rice ( Oryza sativa L.) Varieties as Affected by Heat Treatment. Foods 2023; 12:foods12112207. [PMID: 37297452 DOI: 10.3390/foods12112207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Heat treatment could affect the structure and properties of rice varieties. The present study was conducted in order to determine the effects of heat treatment on the physicochemical properties and tissue structure of Mahsuri Mutan, Basmati 370 and MR219 rice varieties. The three rice varieties were subjected to heat treatment (ageing) at 90 °C, using an oven, for 3 h. After the heat treatment, the samples were cooled at room temperature (25 °C) for 1 h. Physicochemical properties, such as alkali digestion value, water uptake ratio, solids in cooking water, high kernel elongation ratio and amylose contents, were determined. The procedure used in determining both apparent and absolute amylose involved measuring the iodine affinity of defatted whole starch. Ahigh-performance anion-exchange chromatograph was used to analyse branch chain length distribution of amylopectin quantitatively. The starch structure of the rice samples was observed under a scanning electron microscope. Data collected on physicochemical traits, heat treatment and control (ageing and non-ageing) were subjected to an analysis of variance using SAS software version 9.4. In this study, Mahsuri Mutan and Basmati 370 showed superior high kernel elongation as compared to their respective rice progenies. This study also found that heat treatment directly affected the increasingly high kernel elongation for both populations. The phenotypic correlation co-efficient indicated that there was a high positive correlation between high kernel elongation and water uptake ratio, implying that selection for water uptake ratio would increase the high kernel elongation characteristic. The heat treatment showed significant difference in all the physicochemical traits of the varieties studied. Heat treatment also affected the very long branch chains of starch, such as amylose. Observation under an electron microscope showed that the samples subjected to heat treatment had more cracks on the tissue structure compared to normal rice samples. The hexagon structure in Mahsuri Mutan produced a greater elongation effect on its kernel. The findings from this study could be useful to breeders in the selection and development of a new high kernel elongation rice variety.
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Affiliation(s)
- Anna Arina Bt Ab Halim
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohd Y Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Mohamad B Osman
- Malaysia Agriculture Research and Development Institute (MARDI), Serdang 43400, Selangor, Malaysia
| | - Samuel C Chukwu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki PMB 053, Nigeria
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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Zhang J, Pan D, Fan Z, Yu H, Jiang L, Lv S, Sun B, Chen W, Mao X, Liu Q, Li C. Genetic diversity of wild rice accessions ( Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection. FRONTIERS IN PLANT SCIENCE 2022; 13:999454. [PMID: 36262660 PMCID: PMC9576158 DOI: 10.3389/fpls.2022.999454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/02/2022] [Indexed: 05/28/2023]
Abstract
Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei's diversity index and Shannon-Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.
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Affiliation(s)
- Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- *Correspondence: Qing Liu, ; Chen Li,
| | - Chen Li
- *Correspondence: Qing Liu, ; Chen Li,
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Ageing Effects, Generation Means, and Path Coefficient Analyses on High Kernel Elongation in Mahsuri Mutan and Basmati 370 Rice Populations. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8350136. [PMID: 34095311 PMCID: PMC8164538 DOI: 10.1155/2021/8350136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/10/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022]
Abstract
High kernel elongation (HKE) is one of the high-quality characteristics in rice. The objectives of this study were to determine the effects of ageing treatments, gene actions, and inheritance pattern of kernel elongation on cooking quality in two populations of rice and determine the path of influence and contribution of other traits to kernel elongation in rice. Two rice populations derived from crosses between MR219 × Mahsuri Mutan and MR219 × Basmati 370 were used. The breeding materials included two F1 progenies from the two populations, and their respective parents were grown in four different batches at a week interval to synchronize the flowering between the female and male plants. Scaling tests and generation means analysis were carried out to determine ageing effects and estimate additive-dominance gene action and epistasis. The estimation of gene interaction was based on quantitative traits. Path coefficient analysis was done using SAS software version 9.4 to determine the path of influence (direct or indirect) of six quantitative traits on HKE. Results obtained showed that nonallelic gene interaction was observed in all traits. The results before ageing and after ageing showed significant differences in all traits, while the gene interaction changed after ageing. The HKE value improved after ageing, suggesting that ageing is an external factor that could influence gene expression. The epistasis effect for HKE obtained from the cross Mahsuri Mutan × MR219 showed duplicate epistasis while that obtained from a cross between Basmati 370 × MR219 showed complimentary epistasis. Besides, the heritability of HKE was higher in Basmati 370 × MR219 compared to that obtained in Mahsuri Mutan × MR219. The path analysis showed that the cooked grain length and length-width ratio positively significantly affected HKE. It was concluded that ageing treatment is an external factor that could improve the expression of HKE. The findings from this study would be useful to breeders in the selection and development of new specialty (HKE) rice varieties.
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Muhammad I, Musa I, Ahmed M, Jatto MI, Yusuf BR. Recovery of Recurrent Parent Genome in a Marker-Assisted Backcrossing Against Rice Blast and Blight Infections Using Functional Markers and SSRs. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9111411. [PMID: 33105815 PMCID: PMC7690635 DOI: 10.3390/plants9111411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/28/2020] [Accepted: 10/20/2020] [Indexed: 05/30/2023]
Abstract
The most vital aspect of marker-assisted backcross breeding is the recurrent parent genome recovery. This enables the selection of only parents with recovered recipient/recurrent parent genome in addition to the targeted genes. The recurrent parent genome recovery (RPGR) ensures that non-desirable genomic segments are removed while the gene of interest is sustained in the recombined progenies without further segregations. This work was aimed at quantifying the RPGR of backcross populations with introgression of bacterial leaf blight resistance genes. Putra-1, a Malaysian elite variety, high yielding with inherent resistance to blast but susceptible to bacterial leaf blight (BLB), was crossed with IRBB60 which is resistant to BLB disease. The IRBB60 has four Xoo resistance genes-Xa4, xa5, xa13 and Xa21. Tightly linked polymorphic functional and SSR markers were used for foreground selection at every stage of backcrossing to select progenies with introgressed target genes. Background selection was done to quantify the percentage of RPGR in the selected lines using 79 confirmed polymorphic microsatellites. Result obtained showed that the percentage of RPGR was 80.11% at BC1F1, 95.30% at BC2F1 and 95.9% at BC2F2. The introgression of Xa4, xa5, xa13 and Xa21 Xoo resistance genes were faster through the adopted marker-assisted backcross breeding compared to what could be obtained through conventional breeding. All the 16 selected lines displayed resistance to BLB with three lines showing high resistance to the disease. The blast resistance contained in the genetic background of Putra-1 was also sustained in all the selected lines. The newly developed lines were recommended as new rice varieties for commercial cultivation.
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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 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki PMB 053, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Yusuff Oladosu
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Isma’ila Muhammad
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Ibrahim Musa
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Muideen Ahmed
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Muhammed Itopa Jatto
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
| | - Bashir Rini Yusuf
- Laboratory of Climate Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (S.C.C.); (Y.O.); (I.M.); (I.M.); (M.A.); (M.I.J.); (B.R.Y.)
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