CHEMOMETRIC ANALYSIS OF OIL PALM (Elaeis guineensis Jacq.) GERMPLASM FROM SENEGAL AND GAMBIA Hana Saleh Alhadi Abdarhman (Matric No. 3130043) Dissertation submitted in partial fulfillment for the degree of MASTER OF SCIENCE (FOOD BIOTECHNOLOGY) Faculty of Science and Technology UNIVERSITI SAINS ISLAM MALAYSIA Nilai May 2015 ii AUTHOR DECLARATION I hereby declare that the work in this dissertation is my own except for quotations and summaries which have been duly acknowledged. Date: 15thMay, 2015 Signature: Name: Hana Saleh Alhadi Abdarhman Matric No: 3130043 Address: P6-11A-05 Plaza Indh Sepakat Indah1, Kajang 43000, Selangor iii BIODATA OF AUTHOR Hana Saleh Alhadi (Matric No. 3130043) was born on 8th February, 1988. She is a Libyan by Nationality. She is currently living at P6-11A-05 Plasa Indah Apartment Sepkat Indah 1, Kajang, Selangor, Malaysia. She obtained her Bachelor of Science (Botany) from 7th October University, Bani Walid, Libya. Being an enthusiastic person, with the purpose of exploring knowledge and skill of the field she enrolled in September, 2013 for her Master Degree in Food Biotechnology at Universiti Sains Islam Malaysia, Bandar Baru Nilai, Malaysia. She can be contacted by email via (hs.zbida@yahoo.com). iv ACKNOWLEDGEMENTS My first and foremost thanks is to Allah (SWT) who has made all things possible. I would like to express my gratitude to my supervisor Emeritus Professor Dr. Jalani Sukaimi for the useful comments, remarks and engagement through the learning process of this master dissertation. Your advice on both research as well as on my career have been priceless. Furthermore, I would like to thank my co-supervisor, Dr. Mohd Sukri Hassan for his supervisor on chemometrics for my thesis. Also, I would like to thank staff of the Faculty of Science and Technology of the university; the Dean of the faculty, Prof. Bachok Taib, staff of Food Biotechnology, laboratory assistants and technicians of the faculty. I am thankful for their aspiring guidance, invaluably constructive criticism and friendly advice during my study. I am sincerely grateful to them for sharing their truthful and illuminating views on a number of issues related to the research and career. A special thanks to my family. Words cannot express how grateful I am to my mother, father, brothers and sisters for all of the sacrifices that you’ve made on my behalf. Your prayer for me was what sustained me thus far. At the end I would like express appreciation to the Government of Libya for financial support of my studies. Without you, my appreciation would not be completed. v ABSTRAK Anggaran kepelbagaian genetik dan menentukan hubungan antara koleksi adalah strategi yang penting untuk memastikan pengumpulan dan penggunaan germplasma yang cekap. Bahan germplasma sawit yang dikutip dari Senegal dan Gambia yang ditanam di Stesen Kluang MPOB telah dicirikan mengikut kepelbagaian genetik. Sebanyak 44 ciri - ciri agronomi germplasma sawit ini telah dinilai melalui statistik yang mudah untuk menilai kepelbagaian genetik; dan dua teknik kemometrik (PCA dan analisis Kluster) untuk mengenal pasti sifat - sifat yang menyumbang kepada perubahan keseluruhan dan mengklasifikasikan bahan-bahan itu berdasarkan persamaan. Keputusan profil kepelbagaian itu menunjukkan bahawa germplasma kelapa sawit Senegal dan Gambia mempunyai kebole hubahan yang rendah kepada tinggi untuk pelbagai ciri. Sembilan komponen utama dengan nilai eigen > 1 bersamaan dengan 88% daripada jumlah variasi dengan majoriti variasi itu dikuasai oleh PC1. Kebanyakan ciri-ciri, khususnya, BTS, ABW, BWT, MFW, P / B, M / F, OY, TEP, TDM, BDM, e, S / F, K / F, O / B dan K / B menyumbang kepada kepelbagaian di antara dan dalam germplasma, yang mana menunjukkan bahawa variasi yang luas wujud dalam bahan germplasma yang telah dikaji. Analisis kumpulan Ward adalah berdasarkan keputusan - keputusan PCA yang telah dikumpulkan untuk aksesi 42 minyak kelapa sawit kepada enam kelompok, dan kelompok-VI mempunyai bilangan tertinggi ahli. Tambahan pula, ia tiada kaitan antara kepelbagaian genetik dan asal geografi. Purata ciri-ciri agronomi setiap kelompok menunjukkan bahawa kelompok-III mempunyai nilai purata tertinggi pada sifat hasilnya. Selain itu, kumpulan - kumpulan kelompok yang mempunyai nilai purata yang tinggi bagi ciri-ciri yang diingini boleh dipilih untuk ciri-ciri setiap satu. Pengaksesan ini boleh digunakan untuk menghasilkan bahan-bahan kelapa sawit yang berhasil tinggi. Kata kunci: Kelapa sawit, germplasma, kepelbagaian genetik, kimometrik, analisis komponen utama, analisis kelompok. vi ABSTRACT Estimation of genetic diversity and determination of the relationships between collections are useful strategies for ensuring efficient germplasm collection and utilization. Oil palm germplasm materials collected from Senegal and Gambia maintained at the MPOB Kluang Station were characterized for genetic diversity. A total of 44 agronomic traits of these oil palm materials were subjected to simple statistics to evaluate the genetic variability; and two chemometric techniques (PCA and Cluster analysis) to identify the characters contributing to the overall variation and classify the materials based on similarity. Results of the variability profile showed that the Senegal and Gambia oil palm germplasm exhibited low to high variability for the various traits. Nine principal components with eigenvalue >1 accounted for 88 % of the total variation with PC1 capturing majority of the variation. Most of the traits especially, FFB, ABW, BWT, MFW, P/B, M/F, OY, TEP, TDM, BDM, e, S/F, K/F, O/B and K/B contributed to divergence between and within the germplasm, indicating that wide variation exists in the germplasm materials studied. Ward’s cluster analysis based on the PCA results grouped the 42 oil palm accessions into six clusters with cluster-VI having the highest number of members. Furthermore, there was no association between genetic diversity and geographical origin. Means of the agronomic traits of each cluster showed that cluster-III had the highest mean value of yield traits. Also, the cluster groups having high mean values for desired traits could be selected for the traits per se. These accessions could be used to produce high yielding oil palm materials. Keywords: Oil palm, germplasm, genetic diversity, chemometrics, principal component analysis, cluster analysis. iiv ملخص البحث والاستفادة الوراثية المادة جمع لضمان مفيدة استراتيجيات هي المجموعات بين العلاقات وتحديد الوراثي التنوع تقدير في gnaulK BOPMمن محطة وغامبيا السنغال من جمعها تم التي الزيت لنخيل الوراثية الأصول مواد تميزت. منها .الوراثي التباين لتقييم بسيطة لإحصاءات النخيل لزيت الزراعية من الصفات 44 وتعرض. الجيني الحفاظ علي التنوع الاختلاف في المساهمة الشخصيات على للتعرف) )ACالعنقودي والتحليل )ACP( الرئيسيوتقنيات تحليل المكون لنخيل الوراثية الأصول ) أن ACP( نتائج تحليل المكون الرئيسي وأظهرت . التشابه أساس على المواد وتصنيف الكلي تمثل 1 < الذاتية القيمة مع رئيسية عناصر تسعة. الصفات لمختلف كبير تفاوت عرضت وغامبيا من السنغال الزيت ,WFM ,TWB ,WBA BFF خاصة، الصفات معظم ساهم. 1CPوأغلب الاختلاف من الكلي التباين من٪ 88 الوراثية، المادة بين الاختلاف إلى B / Kو ,B / O ,F / K ,F / S ,MDB ,MDT P,ET ,YO F ,/ M ,B / P نتائج على بناء وارد ) )AC العنقودي التحليل . المدروسة الوراثية الأصول مواد في موجود واسع تباين أن إلى مشيرا عدد أكبر تميزت بوجود 5 مجموعات. كتلة الزيت الي ست من نخيل 24حيت تم تقسيم ))ACP تحليل المكون الرئيسي الزراعية الصفات وأظهرت . الجغرافي والأصل الجيني التنوع بين ارتباط هناك يكن لم ذلك على وعلاوة . الأعضاء من زيت المجموعات لإنتاج هذه استخدام ويمكن أيضا. الصفات من العائد متوسطل قيمة أعلى تميزت بوجود 3الكتلة أن . بعوائد عالية ذات النخيل الرئيسي و المكون تحليل ،scirtemomehc الجيني، ،التنوع النخيل لزيت الوراثية الأصول : المفتاحية للبحث كلمات ال . العنقودي التحليل viii CONTENT PAGE Contents Page AUTHOR DECLARATION i BIODATA OF AUTHOR ii ACKNOWLEDGEMENTS iii ABSTRACT v ABSTRACT vi ABSTRACT vii CONTENT PAGE viii LIST OF TABLES xi LIST OF FIGURES xii LIST OF APPENDICES xiii ABBREVIATION xiv CHAPTER I: INTRODUCTION 1 1.1 Problem Statement 2 1.2 Aim 3 1.3 Research Questions 3 1.4 Objectives 3 CHAPTER II: LITERATURE REVIEW 4 2.1 HISTORY OF THE GENUS ELAEIS 4 2.1.1 Evolution of the Genus Elaeis 5 2.1.2 Morphology and Biology of E. guineensis 6 2.1.3 Infra Specific Classification of E. guineensis 7 2.1.4 Ecology and Morphology of E. guineensis 9 2.2 PLANT GENETIC RESOURCES 13 ix 2.2.1 Genetic Diversity 13 2.2.2 Characterization of Genetic Diversity 14 2.3 CHEMOMETRICS 15 2.3.1 Principal Components Analysis (PCA) 16 2.3.1 Clustering Analysis 18 2.3.1.1 Types of Clustering 20 2.4 PREVIOUS STUDIES 21 CHAPTER III: MATERIALS AND METHODS 27 3.1 Breeding Materials and Site Location 27 3.2 Data Collection 27 3.2.1Yield and Yield Components 27 3.2.2 Bunch Analysis 28 3.2.3 Vegetative Measurements and Physiological Characters 30 3.2.4 Fatty Acid Traits 31 3.3 Statistical Analyses 32 3.3.1 Variability Profile 32 3.3.2 Principal Components Analysis (PCA) 33 3.3.3 Cluster Analysis 34 CHAPTER IV: RESULTS 36 4.1 Variability Profile 36 4.2 Principal Components Analysis (PCA) 36 4.2.1 Scores Plot 38 4.2.2 Loadings 38 4.2.3 Scores 42 4.2.4 Bi-Plot 42 4.3 Cluster Analysis 45 4.3.1 Genetic Distance 49 CHAPTER V: DISCUSSION 50 5.1 PCA 50 x 5.1.1 Scores Plot 51 5.1.2 Loadings 51 5.1.3 Scores 53 5.1.4 Bi-Plot 54 5.2 Cluster Analysis 54 5.2.1 Genetic Distance 56 CHAPTER VI: CONCLUSIONS AND RECOMMENDATIONS 57 REFERENCES 59 APPENDIX 65 xi LIST OF TABLES Page Table 1: Extent of Variation 36 Table 2: Variability profile of Senegal and Gambian oil palm germplasm as analyzed by descriptive statistics 37 Table 3: Principal components analysis for Senegal and Gambia oil palm germplasm based on 46 agronomic traits 39 Table 4: Scores of the 42 Senegal-Gambian oil palm germplasm on the extracted PCs 43 Table 5: Characteristics means of six clusters generated by Ward’s cluster analysis based on 46 agronomic traits 48 Table 6: Inter cluster distance as analyzed by proximity matrix of squared Euclidean distance 49 xii LIST OF FIGURES Page Figure 1: Scores plot where PCs 1 and 2 are orthogonal to each other 18 Figure 2: Clustering pattern 19 Figure 3: Scores plot of principal component analysis between percentage variance and number of principal components 38 Figure 4: Scattered diagram of 46 oil palm germplasm traits for first two components contributing almost half of the total variability 41 Figure 5: Scattered diagram of 46 oil palm germplasm traits showing correlation to the first two components 41 Figure 6: Two dimensional ordinations of 42 Senegal-Gambian oil palm accessions on principal axes 1 and 2 44 Figure 7: Bi-plot of 46 oil palm agronomic traits and 42 oil palm accessions on PC 1 and PC 2 44 Figure 8: The relationship among the oil palm germplasm reflected by cluster analysis 46 xiii LIST OF APPENDICES Page Appendix 1: Proximity Matrix of Squared Euclidean Distance 66 xiv ABBREVIATION ABW average bunch weight BNO bunch number BWT bunch weight BDM bunch dry matter BI bunch index C12:0 lauric acid C14:0 myristic acid C16:0 palmitic acid C16:1 palmitoleic acid C18:0 stearic acid C18:1 oleic acid C18:2 linoleic acid C18:3 linolenic acid C20:0 arichidic acid DIAM diameter of trunk e radiation conversion efficiency f fractional interception of radiation F/B fruit/bunch FFB fresh fruit bunch FP frond production GAM Gambia HT height IV iodine value K/B kernel/bunch K/F kernel/fruit KY kernel yield LA leaf area xv LAI leaf area index LL leaflet length LN number of leaflet LW leaf width MARDI Malaysian agricultural research and development institute M/F mesocarp/fruit MFW mean fruit weight MNW mean nut weight MPOB Malaysian palm oil board NAR net area ratio NIFOR Nigerian institute for oil palm research O/B oil/bunch O/DM oil/dry mass O/WM oil/wet mass OY oil yield P/B parthenocarpic fruit/bunch PCA principal component analysis PC(s) principal component(s) PCS petiole cross section PORIM palm oil research institute of Malaysia RL rachis length RRS reciprocal recurrent selection SEN Senegal S/F shell/fruit TEP total economic product TDM total dry mass UPGMA unpair weighted group method using arithmetic averages VDM vegetative dry mass WHCA Ward’s hierarchical clustering analysis