I. Introduction to Plant Breeding

1. I. Introductionto PlantBreeding Outline of plant breeding Basics in plant breeding Plant breeding systems http://cmb.snu.ac.kr/index.asp

2. Outline of plant breeding Worldcropproduction (2011) (단위: 10억$) 2,583 세계시장규모(매출액) 자동차 1,640 (2010) 반도체 315 (2011) 의약품 942 (2011) 우리나라 총예산(2013) 342조원 GDP(2012) 1272조원 (FAOSTAT 외) 3/46

3. Average corn grain yields in the U.S. (U. Nebraska-Lincoln, 2004) 160 140 Single-cross hybrids Grain yield (Bushel/acre) 120 100 80 Open-pollinated vars. 60 40 20 Double-cross hybrids 0 1860 1880 1900 1920 1940 1960 1980 2000 2010 Year

4. NUE of spring barley varieties differing in date of commercial introduction (Ian Bingham et al. 2011, Sustainability and Communities)

5. 주요 선진국의 식량(곡물) 자급율 (%) (우리나라=2010, 외국=2005) 왜 선진국들의 곡물자급율은100%를 상회할까? (농식품부, 2013)

6. Lowerusic acid rapeseed (>20%)  canola (<2%) • Triple low canola: • Lowerusicacid (toxic) • <30 µM glucosinolate (bitter) • <2% acid detergent lignin

7. Rough rice yield and its annual increase by 10-year interval in the world Rough rice yield (ton/ha) 2.6 % Annual increase in the given interval 2.2 % 1.7 % 1.2 % 0.8 %

8. Chronological changes of yield in 3 major cereal crops GM maize Maize Grain yield (ton/ha) Rice Wheat Year interval

9. AVG yield=122 bu The impacts of projected climate change on U.S. crop yields the threshold temperature that limits the growth of crops is assumed to be 32°C. ~30%↓ ~40%↓ AVG yield= 31 bu

10. Simplified representation of the main factors determining yield change and the implication of climate change-anticipating technologies. Nat. Climate Change 2: 153–154 (2012)

12. Sequencial flow of Plant breeding Breeding objectives Germplasm search Creation of variation R & D Breeding methods Selection and genetic fixation Trait evaluation Variety registration Technology Administration Seed multiplication/maintenance Distribution

13. Natural variation Introduction Hybridization(recombination/ accumulation of genes) Land races Pure line var Pure line Breeding Objectives F1 hybrid var Selection (combination/ transgression) Germplasm Inbred line Creation of variation Synthetic var clone Clonal var Variation by crossing Evaluaton Selection method Haploid method Evaluation/ Var registration Mutation GM Chromosome manipulation MAS Cell fusion Multiplication/ Distribution (Molecular breeding) Choice Must Outline of plant breeding procedure

14. Breeding objectives of crops in general

15. + + Outline of advancement of breeding methods Genome Genetics DNA 1900 1953 BC 8,000 AD 1819 2000 1985 1903 1909 1911 1927 1934 1994 Breeding by seperation (Farmers) Cross breeding Breeding by Seperation (Breeders) Heterosis breeding Polyploid breeding Mutation breeding Tissue culture Molecular marker Transgenic crops PCR Molecular map White, Tomato roottip culture Tomato FlvrSavr Chromosome Molecular Breeding

16. Development of plant breeding methods 1800 1900 1920 1940 1960 1980 2000 Introduction Seperation breeding Artificail crossing Use of heterosis Chromosomal variation Induced mutation Tissue culture Cell fusion Transgenic crops Targeted mutagenesis Pedigree/bulk, etc Backcross method Recurrent selection Anther culture Marker assisted selection) Genomic selection Creation of variation Selection methodology 3/48

17. Considerations for choosing breeding methods • Breeding system of target crops : self- or cross-poll. • Variety type : Pure line var, F1 hybrid, Synthetic var • Available germplasm fortargettraits • Genetic information of target traits • Breeding duration • Resources available for breeding • Easiness of trait evaluation

18. Modern Plant Breeding (ISAAA) Is the trait of interest present in close relatives? Yes No Genetic engineering for trait identification Insertion of genes from other organisms Conventional breeding and mutagenesis Mapping of genes involved Development of markers for the gene(s) Screening of cultivars and wild relatives Identification of DNA markers GMO breeding DNA marker-assisted breeding

19. 2. Basics in plant breeding Plant reproduction Hermaphrodite( 양성화) Homogamy(자웅동숙) Self-pollination Sexual R. Cross-pollination Monoecy (단성화) Hermaphrodite(양성화) 자웅이숙(dichogamy) 자가불화합성(SI) 웅성불임성(MS) 장벽수정(hercogamy) Vegeta. propagation Asexual R. Apomixis

20. 700 nm Supercoil (직경 200 nm) 히스톤 (histone) nucleosome (직경 10 nm) 구슬모양 (beads) 직경 30 nm DNA double helix 직경 2nm 중기 염색체 (투과전자현미경사진) Basic genetics DNA (deoxyribonucleicacid): ribose+phosphate+base(4종류)의 polymer RNA (ribonucleic acid) --- TMV 등 일부 기생성 virus

21. (유전정보보유) Structural gene Regulating transcription • Gene : the unit of inheritance • determines the sequence of a given protein • Protein made by reading RNA - ribonucleic acid • messenger - mRNA • transfer - tRNA • ribosomal – rRNA Structure of a plant gene

22. Glossary • Allele – alternate form of a gene • Homozygous – Alleles for trait are identical Heterozygous – Alleles for trait are not identical • Genotype – Organism’s genetic constitution Phenotype - Outward expression of the genotype • Dominant gene(allele) - When genes are heterozygous for a certain trait, one is expressed Recessive gene(allele) - When genes are heterozygous for a certain trait, one is not expressed • Complete dominance: the dominant gene is the only one expressed Incomplete dominance: both genes play into the phenotype, intermediate phenotype

23. Complete Dominance Given: A= Red flowers; a= White flowers Parents: AA x aa Genotypic Ratio Aa- All Phenotypic Ratio Red- All Parents: Aa x aa Genotypic Ratio Aa- 2= 1 aa- 2= 1 Phenotypic Ratio Red- 1 White- 1 Parents: Aa x Aa Genotypic Ratio AA- 1 Aa- 2 aa- 1 Phenotypic Ratio Red- 3 White- 1

24. Incomplete Dominance Given: AA= Red flowers; Aa= Pink flowers; aa= White flowers Parents: AA x aa Genotypic Ratio Aa- All Phenotypic Ratio Pink- All Parents: Aa x aa Genotypic Ratio Aa- 2= 1 aa- 2= 1 Phenotypic Ratio Pink- 1 White- 1 Parents: Aa x Aa Genotypic Ratio AA- 1 Aa- 2 aa- 1 Phenotypic Ratio Red- 1 Pink- 2 White- 1

25. DNA (유전자) Gene (DNA) : 유전정보 보유 mRNA Protein (tRNA) Phenotype 전사조절 transcription processing 전사 핵 Pre-mRNA mRNA가공 mRNA translation processing 세포질 mRNA 세포질로 운발 mRNA 리보솜 mRNA 안정성 조절 아미노산 processing 불활성 mRNA 단백질 합성 및 조절 합성된 단백질 가종 활성/불활성 단백질 Gene expression tRNA 유전정보: 특정 아미노산을 합성하는 정보 --- 3개 염기씩이 1개 아미노산 합성 정보단위 * 아미노산: 20종  결합하여 단백질 구성 가공: mRNA나 합성된 단백질이 쓰여지기 전에 구조 나 기능이 변경되는 것.

26. G G b b Linkage and genetic map P와 b: close(tight) linkage T와 b / t와 b: loose linkage A/G와 t/b/P : independent P와 b, P와 t : repulsion G와 A, t와 b: coupling Crossover (Meiosis I – Prophase)

27. A A a a A A a a X X B B b b B B b b A a A a B b B b A A a a A A a a B b B b B b B b >1/4 >1/4 1/4 1/4 1/4 1/4 <1/4 <1/4 A-a, B-b : if two loci are independent A-a, B-b : if two loci are linked Parents F1 Gametes of F1 plant Gamete ratio 부모형 (parental type) 조환형 (recombinant)

28. Genetic map - Linkage map: 유전자간 연관의 정도(=조환가)를 기초로 제작 - Physical map: 염색체내에서의 유전자간 실제 거리를 기초로 제작 43.4 Mb

29. Linkage and plant breeding • Recombination frequency between genes is directly affected by linkage intensity. • Tight linkage  no recombinant • Loose linkage  lots of recombinants • Close linkage between desirable genes  Easier in gene accumulation through simultaneous selection • Close linkage between a desirable gene and an undesirable gene •  cause a linkage drag  difficult in breeding target genotypes • Information on linkage between genes are useful in breeding fordetermining • -Size of breeding population • - Selection intensity • - Selection methods

30. Quantitative traits P1 P2 P1 P2 P1 P2 P1 P2 한 개의 유전자쌍이 관여 유전력이 낮을수록 연속변이

31. P1 P1 P2 P2 P1 P1 P2 P2 여러 개의 유전자쌍이 관여  연속변이 Theoretical distributions in F2. The model postulates (1) 100 % heritability, (2) That a twelve-unit difference between parents is generated by various numbers of genes of equal effects, (3) no linkage, and (4) that dominance is isodirectional. The scale is not constant.

32. 3. Plant breeding systems Classification of the flowering plant's sexual systems (Poll. mechanism: 11-13)

33. 3. Sex expression of groups of plants Hermaphrodite: a group consisting of only hermaphrodite plants Monoecious: a group consisting of only monoecious plants Dioecious : a group consisting of androecious and gynoecious plants --- hop, spinach, asparagus, hemp, 은행나무 등 Androdioecious: a group consisting of hermaphrodite and androecious plants Gynodioecious: a group consisting of hermaphrodite and gynoecious plants

34. Distribution of sexual systems in angiosperms (Pl Breeding Systems, p.10)

35. Classification of hermaphrodite flower modifications

36. Self- and cross-pollination (or fertilization) ○ From the genetic point of view Self-pollination(autogamy): interfloral-intraplant pollination interplant-intraclonal" (veget-propagated crops) interplant-intravarietal" (Self-pollinated crops) Cross-pollination(allogamy) : pollination between unlike genotypes ○ In breeding point of view Self-pollination : pollination within the same flower Cross-pollination: pollination between different flowers ○ Criteria for classifying self- or cross-pollinated crops - natural outcrossing rate가 less than 1% or4% (wrong) - predominantly self-pollinated crops - predominantly crossf-pollinated crops * inbreeding(同系교배; endogamy): the crossing of genetically-closely related plants or animals outbreeding(異系교배; exogamy; crossbreeding): the crossing of genetically unrelated plants or animals

37. Mechanism of autogamy - Flowers : hermaphrodite -- homogamous ○ Cleistogamy(CL) --- 56 family287 species (Lord 1981 Bot.Rev.47(4):421-449) 70genusin grasses (Corner 1979 NewZealand J Bot 17:547-574) crops: beans, oats, sorghum, wheat, barley, rice a. Ecological cleistogamy: The presence or abscence is conditioned by environmental factors such as drought, heat, cold, shade, nutrition, submersion or burying of flowers, etc. ===> a floral dimorphism of cleisto-chasmogamous types by season 예) lespedeza (Lespedeza stipulacea) -- 21℃의 저온 CL 主, 27℃이상의 고온 CH. rescue grass(Bromuscatharticus)-- dry & hot 조건에서 CL 主 japonica rice -- 다습조건에서 CL 主, 일시적인 저온(15℃) CL sorghum -- 이삭의 끝부분 CL, 중앙과 밑부분 CH

38. b. Constitutional cleistogamy : controlled genetically 예) * panicle이 boot-leaf sheath에 싸여있는 채로 pollinated - rice: Sathi(인도품종) --- Shp-1, Shp-2 Gamadi(네팔품종) --- Shp-3, Shp-4 - annual fescue (Festucamicrostachys) * not flowered due to floral structure--- 대부분 CL이 single recessive. - under-developed lodicules in spikelets : durum wheat, barley, wheat, rice - Floral deformity : peageonpea (enclosedanther within flower) sorghum(papery glume: normal, rolled glume:CL) Lodiculeless rice Gamadi rice

39. ○ Chasmogamicselfing a. Preanthesis self-pollination legumes : Phaseolus vulgaris (common bean), Phaseolusaureus(mungbean), Pisumsativum(garden pea), Arachishypogaea (peanut), Cajanus cajan(peageongea), Glycin max (soybean) 등 Lepidiumsativum (십자화과 garden cress) grasses: rye grass(Loliumtemulentum), wheatgrass(Agropyrontrachycaulum), brome grass(B. carinatus) 등 b. Functional autogamy: Flower structure and flowering habit are optimized for self-pollination. - grain crops: rice, wheat, barley 등 --- 개영전에 화분성숙, 개영직전에 화사 신장 개영과 동시 또는 직전에 anther 열개 되고 화분이 주두위로 떨어짐. - sesame (Sesamumindicum) : 개화와 동시에 pollen shedding하여 주두 덮음. - legumes (soybean, chickpea 등), Arabidopsis thaliana , flax 등 : 개화하면서 화분 열개시 약이 주두주위에 집결되어 있음. - tomato (Lycoperisconesculentum) : 주두의 위치(길이)가 품종간 변이. 짧고 수술로 둘러싸여 있는 경우 자식율 高 & 결과율 高

40. c. mixed cross- and self- pollination - broad bean (Viciafaba) : 타식율이 30% 정도 --- bumble bee(땅벌) 이 꽃에 앉았을 때 rm무게에 의해 생긴 용골판(keel petal)의 틈으로 주두와 약이 튀어나오고, 화분이 방출되어 매개충(다른 꽃에 타식 유발)과 주두에 떨어짐. - peppers (Capsicum annuum, C. frutescens) : 매개충의 빈도와 genotypes에 따라 타식율이 9-32% --- protogyny현상 有 - cotton : Gossypiumhirsutum --- shorter style, 꽃이 open more widely : 40% 정도 타식 G. barbadense --- long style : 5-10% 타식 * Selective fertilization : sunflower(Helianthus annus), raspberry(나무딸기; Rubusidaeus) 등에서는 foreign pollen이 own pollen 보다 수정경쟁(certation)에서 우월 --- 빨리 화분관 신장해서 수정됨. 외래화분이 없을 경우 자식됨.

41. Mechanism of allogamy o Spatial isolation of gametes monoecious crop : maize, strawberry, walnuts, pumpkin, cucumbers, cassava 등 dioecious   "   : hemp, spinach, hop, asparagus, yam, papaya 등 o Dichogamy protandry(웅예선숙) : onions, sugar beets, 도라지, 복숭아, 조롱박, coconut, carrot, beets, raspberry(나무딸기) 등 protogyny(자예선숙) : avocado 등 o Self-incompatability: Brassicas, rye, sunflower, 피만, 서양유채 등 o 웅성불임성 (male sterility) o 장벽수정(hercogamy): 붓꽃과(Iridaceae) ** 자식과 타식의 중간형 (partly allogamy) : 수수, 목화, 해바라기, 피만, 서양유채 등

42. Impact of self- and cross-fertilization on plant characteristics

43. Breeding methods classified by crop breeding systems Self-poll.Cross-poll.Vegetatively prop. Introduction ◯ ◯ ◯ Pure line sel◯ X ◯(seedling) Mass sel△ ◯△ Pedigree method◯△ ◯ (crossing sel  propa) Bulk method◯◯X Backcross method◯◯△ Remote hybridization◯◯◯ Heterosis breeding◯ ◯◯ Mutation breeding◯ ◯ ◯ Chromosome manip. △ △ ◯ Transgenic breeding ◯ ◯ ◯ Marker-assisted breeding ◯ ◯ ◯ ResultsPure line Inbred line,Clone Synthetic variety ◯very frequently, ◯ frequently, △ occasionally, X scarcely

44. Isolation standard in seed production plots (Unit:m) http://edocket.access.gpo.gov/cfr_2005/janqtr/pdf/7cfr201.76.pdf