NCHU Course Outline
Course Name (中) 作物分子育種學(6154)
(Eng.) Crop Molecular Breeding
Offering Dept Department of Agronomy
Course Type Elective Credits 3 Teacher WANG, CHANG-SHENG
Department Master Program in Specialty Crops and Metabolomics/Graduate Language 中/英文 Semester 2025-FALL
Course Description 在全基因體解序後，後基因體時代來臨了，後基因體時代的作物育種為全基因體育種的包含下特性：全基因體學為範疇，多基因的操作，多性狀的導入與選拔，非基因改造的精準育種。.這是現今基因改造及CRISPR基因編輯技術仍無法做到的。本課程包含基礎遺傳學與育種，質與量及複雜性狀的遺傳與操作原理，由誘變育種創造材料開始，由孟德爾遺傳學、分子遺傳學、基因體學應用於作物育種策略之演進，以水稻抗病分子育種為例，依序介紹遺傳與育種之操作原理，結合基因體學New central dogma 新中心定律及其在作物育種之應用，後基因體時代的新中心定則為包含基因體學、轉錄體學蛋白質體學、代謝體學及表型體學之功能基因體學，應用於分子育種學，包含連鎖圖譜之建立與分子標誌之開發，及分子標誌輔助基因堆疊，結合水稻抗白葉枯病，稻熱病及紋枯病之分子育種實例，讓學生了解，現今及未來育種趨勢之理論與實務。未來的育種是全基因體(全體學All O’mics)的育種是一種先設計再育種 (breeding by design)，以全基因體育種估值 (GEBV, genomic estimated breeding value)再進行育種與選拔，是21世紀糧食作物育種趨勢。
介紹作物育種家所需之基本遺傳學、分子遺傳技術、分子標誌與性狀關係、利用分子標誌輔助選拔、標定與選殖性狀基因之原理、轉殖植株所需之理論與實務，藉由原理解說、實例與實驗觀摩、操作，使同學們了解如何利用分子生物技術與分子遺傳理論，進行作物之分子育種。
Following the completion of the whole-genome sequencing, the post-genomic era emerged. Crop breeding in the post-genomic era encompasses the following characteristics of whole-genome breeding: whole-genome science as the scope, multi-gene manipulation, introduction and selection of multiple traits, and non-genetically modified precision breeding. This is something that current genetic modification and CRISPR technologies cannot achieve. This course covers basic genetics and breeding, the inheritance and manipulation of qualitative, quantitative, and complex traits. It starts with the creation of materials through mutagenesis breeding, and the evolution of crop breeding strategies based on Mendelian genetics, molecular genetics, and genomics. Taking rice disease resistance molecular breeding as an example, this course introduces the principles of genetic manipulation and breeding in sequence, combining the New Central Dogma of genomics with its applications in crop breeding. The new central dogma of the post-genomic era is functional genomics, which encompasses genomics, transcriptomics, proteomics, metabolomics, and phenotypic genomics. This approach is applied to molecular breeding, including the establishment of linkage maps and the development of molecular markers, as well as the use of molecular markers for gene stacking. It combines molecular breeding examples of rice resistance to bacterial blight, blast disease, and sheath blight disease, allowing students to understand the theory and practice of current and future breeding trends. The breeding of the future will be all-genomics, which means breeding by design, utilizing genomic estimated breeding value (GEBV) for breeding and selection. This is the breeding trend for cereal crops in the 21st century.
Prerequisites
self-directed learning in the course Y
Relevance of Course Objectives and Core Learning Outcomes(%) Teaching and Assessment Methods for Course Objectives
Course Objectives Competency Indicators Ratio(%) Teaching Methods Assessment Methods
本課程的目的是讓學生能學以致用，自己真的學會操作課程所傳授的技術。所以課程安排以 知難行易 的基礎進行，學習由操作中邊做邊學，配合試驗操作原理，兼顧理論與實務，以達到知行合一的境界。為維持授課與學習品質，因此本課程以12人為限。講義是英文為主歡迎外籍生選課。
topic Discussion/Production
Discussion
Practicum
Lecturing
Written Presentation
Oral Presentation
Assignment
Quiz
Course Content and Homework/Schedule/Tests Schedule
Week Course Content
Week 1 Review on the traditional breeding and methods
Week 2 Genetics required for practice plant breeding
Week 3 The central dogma of genetics
Week 4 The central dogma of plant breeding
Week 5 Germplasm characterization and application in plant improvement in the 21 century
Week 6 Molecular markers and genetics
Week 7 Methods for Mapping genes
Week 8 Development and validation of molecular markers
Week 9 Breeding by design and smart crossing
Week 10 Prediction and selection of plant breeding
Week 11 Marker-assisted selection and gene pyramiding
Week 12 Genomic breeding and genome-wide selection

Marker development and design from linkage mapping
Week 13 Plant breeding with assistance of software
Week 14 Successful examples of plant breeding through molecular approach
Week 15 Marker-assisted selection and genomic selection
Test of functional markers
Week 16 New plant breeding techniques
Examples of crop breeding
Future prospects of plant breeding
Gene pyramiding in MAS
self-directed
learning		    03.Preparing presentations or reports related to industry and academia.
   04.Participation in visits or internships at industry, government, or academic institutions.
   05.Participation in various workshops organized by different departments of NCHU.
Evaluation
I.平時考 30%、期末考 30%、期末報告 30%及指定作業 10%。
II.期末報告須知:
1.文獻報告。
2.繳交期限:報告前一周交 PPT。
Textbook & other References
1.Principles of plant genetics and breeding. 2012. Geroge Acquaah. Wiley-Blackwell.
2.Molecular Plant Breeding. 2010. Yunbi Xu. CABI.
3.Biotechnology-and-Plant-Breeding 2014.

參考文獻
1.Bernardo R. 2010. Genome-wide selection with minimal crossing in self-pollinated crops. Crop Sci. 50: 624-627.
4.Chang, TS, C-S Wang and Chien-Chen Lai et. al. (2017, Nov). Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS. Plant Molecular Biology, 95(4), 333-343. (SCI).
3.Chen, R. K., M. H. Tsai, and K. Y. Chen. 2013. The construction of a random-type SNP molecular marker database for Taiwanese japonica rice varieties. Res Bull Tainan Dist Agric Improv Stn. 61:15-28.
4.Chung, Y. S., and Kim, C. S. et. al. 2017. Genotyping-by-sequencing: a promising tool for plant genetics research and breeding. Hort Environ Biotechnol. 58:425-431.
5.Cobb, J. N., and J. D. Platten et al. 2019. Back to the future: revisiting MAS as a tool for modern plant breeding. Theor Appl Genet. 132:647.
6.Collard, B. C, Y., and D. J. Mackill. 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc. B. 363:557-572.
7.Elshire, R. J., and, Mitchell, S. E., et al. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high-diversity species. PLOS ONE. 6:e19379.
8.Fadiji AE, Santoyo G, Yadav AN and Babalola OO (2022) Efforts towards overcoming drought stress in crops: Revisiting the mechanisms employed by plant growth-promoting bacteria. Front. Microbiol. 13:962427.
9.Godwin,I.D., J. and I.T.Hickey., et al. 2019. Technological perspectives for plant breeding. Theor Appl Genet,132:555-557.
10.Ghazy, M.I., and Sallam, A. et. al. Utilization of genetic diversity and marker-trait to improve drought tolerance in rice (Oryza sativa L.). Mol Biol Rep 48, 157–170 (2021).
11.Huang, M., and C. H. Sneller., et. al. 2019. Use of genomic selection in breeding rice (Oryza sativa L.) for resistance to rice blast (Magnaporthe oryzae). Molecular Breed. 39:114.
12.Lo, K. L and C S Wang et. al. 2022. Two genomic regions of a sodium azide-induced rice mutant confer broad-spectrum and durable resistance to blast disease. Rice. 15:2. (SCI).
13.Meuwissen, T. H. E, and M. E. Goddard. Et. al. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 157:1819-1829.
14.Mir, RR, and RK Varshney., et al. 2012 Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theoretical and Applied Genetics 125, 625-645.
15.Morris, G. P., S. P. Deshpande, and et. al. 2013. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA.110:453-458.
16.Muthu V, and, Kambale R, et al. (2020) Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker-assisted breeding. PLoS ONE 15(1): e0227421.https://doi.org/10.1371/journal.pone.0227421
17.Nakaya, A., and S. N. Isobe. 2012. Will genomic selection be a practical method for plant breeding? Ann Bot. 110:1303-1316.
18.Newell, M. A., and J. L. Jannink. 2014. Genomic selection in plant breeding. Methods Mol Biol. 1145:117-130.
19.Poland, J. A., and T. W. Rife. 2012. Genotyping- by-sequencing for plant breeding and genetics. Plant Genome. 5:92-102.
20.Rasheed, A., Y. and Z. He. Et al. 2017. Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Mol Plant. 10:1047-1064.
21.Ribaut, J. M., and X. Delannay., et. al. 2010. Molecular breeding in developing countries: challenges and perspectives. Curr Opin Plant Biol. 13: 213-218.
22.Soto-Cerda, B. J., and S. Cloutier. 2012. Association mapping in plant genomes. InTech. DOI: 10.5772/33005.
23.Wang, C. S. and Lin, D. G. 2017. The application of genomic approaches in studying a bacterialblight-resistant mutant in rice. Advances in International Rice Research (ISBN:978-953-51-3010-9). InTech. DOI: 10.5772/67331.
24.Wang, C S et al. 2019. Sodium azide mutagenesis generated diverse and broad-spectrum blast resistance mutants in rice. Euphytica 215:145-156.
25.Xiong, W. and Y. Xu, et. al. Climate change challenges plant breeding. Current Opinion in Plant Biology 2022, 70: 102308.
26.Zingaretti, S. M. et al. 2013 Water Stress and Agriculture.http://dx.doi.org/10.5772/53877.
27.王強生 2021. 全基因體分析與先設計再育種—基因體育種是後基因體時代糧食作物的育種趨勢。前瞻基因體學技術於農業領域之研發應用與展望(ISBN:978-986-5452-17-9)(PP.7-26)。
28.王強生 2023.『因應氣候變遷之作物育種』. 2023 112年度農業生態系長期生態研究研討會,112年7月7日台南區農業改良場。
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