PREDICTIVE HYBRIDIZATION OF

ORPHAN CROPS USING

MACHINE LEARNING MODELS

22UCS407/IDEA & DESIGN SPRINT REPORT

Submitted by

JUSTIN VARGHESE - 710723104037

KANISHKA V - 710723104040
KEVIN K R - 710723104047
MAHASMRITI S S - 710723104057

in partial fulfillment for the award of the degree

of

BACHELOR OF ENGINEERING

in

COMPUTER SCIENCE AND ENGINEERING

Dr. N.G.P INSTITUTE OF TECHNOLOGY, COIMBATORE - 641048

AN AUTONOMOUS INSTITUTION

ANNA UNIVERSITY: CHENNAI 600 025

MAY 2025

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 ANNA UNIVERSITY: CHENNAI 600 025

BONAFIDE CERTIFICATE

Certified that this Report titled “PREDICTIVE HYBRIDIZATION OF

ORPHAN CROPS USING MACHINE LEARNING MODELS ” is the
bonafide work of JUSTIN VARGHESE (710720104037), KANISHKA V
(710720104040), KEVIN K R(710720104047) and MAHASMRITI S S
(710720104057) who carried out the work under my supervision.

SIGNATURE SIGNATURE
HEAD OF THE DEPARTMENT SUPERVISOR
Dr. D.PALANIKKUMAR M.E, Ph.D. Dr. L.SRINIVASAN M.Tech,Ph.D.
Professor & Head, Associate Professor,
Department of Computer Science and Department of Computer Science
Engineering, and Engineering,

Dr. N. G. P Institute of Technology, Dr. N. G. P Institute of Technology,

Coimbatore-641048. Coimbatore-641048.

Submitted for the End Semester Idea & Design Sprint Viva-Voce Examination held
on___________________.

____________ _____________

INTERNAL EXAMINER EXTERNAL EXAMINER

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 DECLARATION

I hereby declare that the project work entitled “PREDICTIVE HYBRIDIZATION OF

ORPHAN CROPS USINGMACHINE LEARNING MODELS” submitted to the
autonomous 22UCS407/Idea & Design sprint viva voce – June 2025 is the report of the
original project work done by me under the guidance of Dr. L. SRINIVASAN M.Tech,
Ph.D. Associate Professor, Department of Computer Science and Engineering, Dr.N.G.P
Institute of Technology, Coimbatore- 641 048.

NAME SIGNATURE

JUSTIN VARGHESE _________________________

KANISHKA V _________________________
KEVIN K R _________________________
MAHASMRITI S S _________________________

I certify that the declaration made by the above candidate is true.

Project Guide
Dr. L. SRINIVASAN M.Tech, Ph.D.
Associate Professor,
Department of Computer Science and
Engineering,
Dr. N. G. P Institute of Technology,
Coimbatore-641048.

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 ACKNOWLEDGEMENT

Words act as a gateway to express tokens of acknowledgement. First of all, we

would like to thank the supreme power, our Parents and Almighty God, who has given

us the strength and courage to complete our work successfully.

We would like to express our profound gratitude and deep sense of thanks to

Dr. Nalla G. Palaniswami MD., AB (USA), Chairman of Kovai Medical Center &

Hospital, for providing us with the necessary facilities to complete our project work

effectively.

Our heartfelt gratitude to Dr. Thavamani D Palaniswami MD., AB (USA),

Secretary of Dr. N. G. P. Institute of Technology, for his generous attitude and constant

motivation, which had been one of the sole reasons for completing our project.

We are sincerely grateful to Dr. S. U. Prabha M.E, Ph.D. Principal who has always

been a source of inspiration, well-wisher and a pillar of support for all the students in

our institution by rendering full motivation always.

We are highly indebted to Dr. D. Palanikkumar M.E, Ph.D. Professor and Head of

the Department, Department of Computer Science and Engineering, for his dedication,

keen interest and overwhelming attitude to help his students that have helped us to a

very great extent to accomplish this task.

We wish to thank our Idea & Design Sprint Coordinator Ms.R.P.Shermy, M.E,

Assistant Professor, Department of Computer Science and Engineering, for her

excellent assistance, aspiring guidance, regular feedback and invaluably constructive

ideas.

We express our hearty thanks to our Project Guide Dr. L. SRINIVASAN M.Tech,

Ph.D. Associate professor, Department of Computer Science and Engineering, for his

valuable guidance and timely help for completing our project.

Finally, we owe huge thanks to our teaching Faculty members and Non- teaching

staff members, whose love and insights have so deeply enriched our work.

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 ABSTRACT

In drought-prone regions, conventional breeding methods struggle to produce climate-

resilient crops efficiently, often taking years through trial-and-error approaches. To

address this challenge, this project integrates DNA sequencing, Evolutionary Algorithms

(EA), and Reinforcement Learning (RL) to optimize hybridization in orphan crops—

nutrient-rich but underutilized plants crucial for food security and biodiversity.

This machine learning-driven framework employs EA to simulate natural evolution,

generating genetically diverse hybrids through crossover and mutation. Concurrently, RL

optimizes hybrid selection by analyzing multi-generational performance data, ensuring

superior traits such as high yield, enhanced disease resistance, and adaptability to adverse

environmental conditions. This methodology significantly reduces breeding time compared

to traditional methods while maximizing agronomic potential.

By integrating genetic information with real-time environmental data, the proposed model

enhances breeding efficiency, enabling the development of climate-resilient crops capable

of withstanding extreme weather events, pest infestations, and soil degradation. The

incorporation of large-scale open datasets further strengthens scalability and real-world

applicability. This cost-effective machine learning approach provides a transformative

tool for farmers, researchers, and policymakers, facilitating a sustainable, data-driven

pathway to global food security and resilient agriculture.

Keywords: Machine learning, DNA sequencing, Evolutionary Algorithms (EA),

Reinforcement Learning (RL), hybrid crop prediction, food security, climate resilience,

agronomic potential.

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 LIST OF ABBREVIATIONS

ACRONYMS ABBREVIATIONS

GWAS – Genome-Wide Association Study

SNP – Single Nucleotide Polymorphism

QTL – Quantitative Trait Loci

HMM – Hidden Markov Model

ANN – Artificial Neural Network (specific to

hybridization prediction)

RIL – Recombinant Inbred Line

MAS – Marker-Assisted Selection

GS – Genomic Selection

NIRS – Near-Infrared Spectroscopy

GxE – Genotype-by-Environment Interaction

PCA – Principal Component Analysis

DNN – Deep Neural Network

RF – Random Forest

k-mers – Short DNA Sequence Substrings Used

in Genomic Analysis

SVM – Support Vector Machine

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 TABLE OF CONTENTS

CHAPTER NO TITLE PAGE NO

ABSTRACT
LIST OF FIGURES
LIST OF ABBREVIATIONS

1 INTRODUCTION

1.1 Overview of Hybridization in Agriculture

1.2 Orphan Crops and Their Importance
1.3 Challenges in Traditional Crop Hybridization
1.4 Role of Machine Learning (ML) in Plant Breeding
1.5 ML Algorithms in Hybrid Crop Prediction
1.6 Need for Predictive Hybridization Models
1.7 Objectives of the Project
1.8 Organization of the Report
1.9 Summary

2 LITERATURE REVIEW
2.1 Introduction
2.2 Machine Learning in Agriculture
2.3 Predictive Modeling for Hybrid Crops
2.4 Feature Selection Techniques in Plant Trait Prediction
2.5 Studies on Orphan Crops and Yield Improvement
2.6 Gaps in Existing Research
2.7 Summary

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3 PROBLEM STATEMENT AND PROPOSED SYSTEM
3.1 Introduction
3.2 Limitations of Traditional Hybridization Methods
3.3 Problem Statement
3.4 Proposed Machine Learning-Based Hybridization
3.5 Expected Advantages Over Traditional Methods
3.6 System Architecture Overview
3.7 Summary

4 SYSTEM SPECIFICATION
4.1 Introduction
4.2 Hardware Requirements
4.3 Software Requirements
4.4 Machine Learning Frameworks Used
4.5 Dataset Description and Collection
4.6 Preprocessing of Plant Trait Data
4.7 Summary

5 PROPOSED METHODOLOGY
5.1 Introduction
5.2 Modules of the System
5.2.1 Parent Plant Trait Extraction
5.2.2 Feature Engineering for Hybrid Prediction
5.2.3 Machine Learning Model Training
5.2.4 Random Forest for Hybrid Trait Prediction
5.2.5 Comparison with Other ML Algorithms
5.2.6 Model Evaluation Metrics
5.2.7 Deployment of the Model
5.3 Summary

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6 IMPLEMENTATION AND RESULTS
6.1 Implementation of Machine Learning Models
6.2 Dataset Splitting and Training Process
6.3 Performance Analysis of Hybrid Predictions
6.4 Evaluation Metrics: Accuracy, Precision, and Recall
6.5 Hybrid Crop Yield Prediction Results
6.6 Comparison of Model Performance
6.7 Summary

7 CONCLUSION AND FUTURE WORK

7.1 Conclusion
7.2 Future Work and Enhancements

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