Advances in Oat Genomic Research and Molecular Breeding

doi:10.11983/CBB22182

Abstract

Abstract: Oat (Avena sativa) is an annual grass species grown as either a grain or a forage crop. Its valuable nutrition and excellent forage quality make its market demand increase year by year, which brings forth new requirements for innovative oat cultivars. Molecular breeding is the ideal technology for oat improvement with its high precision and efficiency. Genomic study of oat is the very important basis for the analysis of important agronomic traits, the precise utilization of excellent germplasm and molecular design breeding of oats. This article mainly reviews the important achievements of world-wide oat germplasm resources collection and preservation, genome composition and chromosome ploidy level variations in the genus Avena, oat genetic linkage map construction and oat genome sequencing, as well as oat molecular breeding. Furthermore, this article discusses the future directions of oat genomic study and molecular breeding in the post genomic era.

Key words: oat, genetic linkage map, genome sequencing, molecular breeding

Bo Zhang, Changzhong Ren. Advances in Oat Genomic Research and Molecular Breeding[J]. Chinese Bulletin of Botany, 2022, 57(6): 785-791.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.chinbullbotany.com/EN/10.11983/CBB22182

https://www.chinbullbotany.com/EN/Y2022/V57/I6/785

References 48

[1]	高树琴, 王竑晟, 段瑞, 景海春, 方精云 (2020). 关于加大在中低产田发展草牧业的思考. 中国科学院院刊 35, 166-174.
[2]	李颖, 毛培胜 (2013). 燕麦种质资源研究进展. 安徽农业科学 41, 72-76.
[3]	刘韬 (2021). 燕麦种质资源多样性分析及籽粒皮、裸性状形成的生理和分子机制研究. 博士论文. 北京: 中国科学院大学. pp. 15-16.
[4]	欧斯特, 蒋建平 (2012). 中国燕麦产业发展研究报告. 北京: 中国科学技术出版社. pp. 15-16.
[5]	潘莹, 程时锋 (2021). 燕麦基因组学研究进展. 植物遗传资源学报 22, 304-308.
[6]	任长忠, 崔林, 杨才, 田长叶, 付晓峰, 刘彦明, 赵桂琴, 郭来春 (2016). 我国燕麦高效育种技术体系创建与应用. 中国农业科技导报 18, 1-6.
[7]	任长忠, 胡跃高 (2013). 中国燕麦学. 北京: 中国农业出版社. pp. 49.
[8]	宋高原, 霍朋杰, 吴斌, 张宗文 (2014). 裸燕麦籽粒性状的QTL分析. 植物遗传资源学报 15, 1034-1039.
[9]	吴斌, 张茜, 宋高原, 陈新, 张宗文 (2014). 裸燕麦SSR标记连锁群图谱的构建及β-葡聚糖含量QTL的定位. 中国农业科学 47, 1208-1215.
[10]	吴斌, 郑殿升, 严威凯, 申状状, 晏林, 张宗文 (2019). 燕麦分子育种研究进展. 植物遗传资源学报 20, 485-495.
[11]	Admassu-Yimer B, Bonman JM, Esvelt Klos K (2018). Mapping of crown rust resistance gene Pc53 in oat (Avena sativa). PLoS One 13, e0209105.
[12]	Baum BR (1997). Oats: Wild and Cultivated: A Monograph of the Genus Avena L. (Poaceae). Ottawa: Biosystematics Research Institute. pp. 1-463.
[13]	Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA (2018). Haplotype-based genotyping-by-sequencing in oat genome research. Plant Biotechnol J 16, 1452-1463. DOI PMID
[14]	Chaffin AS, Huang YF, Smith S, Bekele WA, Babiker E, Gnanesh BN, Foresman BJ, Blanchard SG, Jay JJ, Reid RW, Wight CP, Chao S, Oliver R, Islamovic E, Kolb FL, McCartney C, Mitchell Fetch JW, Beattie AD, Bjørnstad Å, Bonman JM, Langdon T, Howarth CJ, Brouwer CR, Jellen EN, Klos KE, Poland JA, Hsieh TF, Brown R, Jackson E, Schlueter JA, Tinker NA (2016). A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. Plant Genome 9, 1-21.
[15]	Cho MJ, Jiang W, Lemaux PG (1999). High frequency transformation of oat via microprojectile bombardment of seed-derived highly regenerative cultures. Plant Sci 148, 9-17.
[16]	Dattgonde N, Tiwari S, Sapre S, Gontia-Mishra I (2019). Genetic transformation of oat mediated by Agrobacterium is enhanced with sonication and vacuum infiltration. Iran J Biotechnol 17, e1563.
[17]	FAO (2010). The second report on the state of the world’s plant genetic resources for food and agriculture. Rome: FAO. pp. 62.
[18]	Gasparis S, Bregier C, Orczyk W, Nadolska-Orczyk A (2008). Agrobacterium-mediated transformation of oat (Avena sativa L.) cultivars via immature embryo and leaf explants. Plant Cell Rep 27, 1721-1729.
[19]	Gless C, Lörz H, Jähne-Gärtner A (1998). Transgenic oat plants obtained at high efficiency by microprojectile bombardment of leaf base segments. J Plant Physiol 152, 151-157.
[20]	Gnanesh BN, McCartney CA, Eckstein PE, Mitchell Fetch JW, Menzies JG, Beattie AD (2015). Genetic analysis and molecular mapping of a seedling crown rust resistance gene in oat. Theor Appl Genet 128, 247-258. DOI PMID
[21]	Gnanesh BN, Mitchell Fetch J, Menzies JG, Beattie AD, Eckstein PE, McCartney CA (2013). Chromosome location and allele-specific PCR markers for marker-assisted selection of the oat crown rust resistance gene Pc91. Mol Breed 32, 679-686.
[22]	Herrmann MH, Mohler V (2018). Locating two novel genes for resistance to powdery mildew from Avena byzantina in the oat genome. Plant Breed 137, 832-838.
[23]	Herrmann MH, Yu JZ, Beuch S, Weber WE (2014). Quantitative trait loci for quality and agronomic traits in two advanced backcross populations in oat (Avena sativa L.). Plant Breed 133, 588-601.
[24]	Kamal N, Tsardakas Renhuldt N, Bentzer J, Gundlach H, Haberer G, Juhász A, Lux T, Bose U, Tye-Din JA, Lang D, van Gessel N, Reski R, Fu YB, Spégel P, Ceplitis A, Himmelbach A, Waters AJ, Bekele WA, Colgrave ML, Hansson M, Stein N, Mayer KFX, Jellen EN, Maughan PJ, Tinker NA, Mascher M, Olsson O, Spannagl M, Sirijovski N (2022). The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature 606, 113-119.
[25]	Kebede AZ, Friesen-Enns J, Gnanesh BN, Menzies JG, Mitchell Fetch JW, Chong J, Beattie AD, Paczos-Grzęda E, McCartney CA (2019). Mapping oat crown rust resistance gene Pc45 confirms association with PcKM. G3 (Bethesda) 9, 505-511.
[26]	Kremer CA, Lee M, Holland JB (2001). A restriction fragment length polymorphism based linkage map of a diploid Avena recombinant inbred line population. Genome 44, 192-204. PMID
[27]	Ladizinsky G (1998). A new species of Avena from Sicily, possibly the tetraploid progenitor of hexaploid oats. Genet Resour Crop Evol 45, 263-269.
[28]	Li Y, Leveau A, Zhao Q, Feng Q, Lu HY, Miao JS, Xue ZY, Martin AC, Wegel E, Wang J, Orme A, Rey MD, Karafiátová M, Vrána J, Steuernagel B, Joynson R, Owen C, Reed J, Louveau T, Stephenson MJ, Zhang L, Huang XH, Huang T, Fan DL, Zhou CC, Tian QL, Li WJ, Lu YQ, Chen JY, Zhao Y, Lu Y, Zhu CR, Liu ZH, Polturak G, Casson R, Hill L, Moore G, Melton R, Hall N, Wulff BBH, Doležel J, Langdon T, Han B, Osbourn A (2021). Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. Nat Commun 12, 2563. DOI PMID
[29]	Liang XD, Shalapy M, Zhao SF, Liu JH, Wang JY (2021). A stress-responsive transcription factor PeNAC1 regulating beta-D-glucan biosynthetic genes enhances salt tolerance in oat. Planta 254, 130.
[30]	Maqbool S, Zhong H, El-Maghraby Y, Ahmad A, Chai B, Wang W, Sabzikar R, Sticklen M (2002). Competence of oat (Avena sativa L.) shoot apical meristems for integrative transformation, inherited expression, and osmotic tolerance of transgenic lines containing hva1. Theor Appl Genet 105, 201-208. PMID
[31]	Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN (2019). Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 17, 92. DOI PMID
[32]	Ociepa T, Okoń S, Nucia A, Leśniowska-Nowak J, Paczos-Grzęda E, Bisaga M (2020). Molecular identification and chromosomal localization of new powdery mildew resistance gene Pm11 in oat. Theor Appl Genet 133, 179-185.
[33]	O’Donoughue LS, Sorrells ME, Tanksley SD, Autrique E, Deynze AV, Kianian SF, Phillips RL, Wu B, Rines HW, Rayapati PJ, Lee M, Penner GA, Fedak G, Molnar SJ, Hoffman D, Salas CA (1995). A molecular linkage map of cultivated oat. Genome 38, 368-380. PMID
[34]	Okoń SM, Ociepa T (2018). Effectiveness of new sources of resistance against oat powdery mildew identified in A. sterilis. J Plant Dis Prot 125, 505-510.
[35]	Oliver RE, Tinker NA, Lazo GR, Chao S, Jellen EN, Carson ML, Rines HW, Obert DE, Lutz JD, Shackelford I, Korol AB, Wight CP, Gardner KM, Hattori J, Beattie AD, Bjørnstad Å, Bonman JM, Jannink JL, Sorrells ME, Brown-Guedira GL, Mitchell Fetch JW, Harrison SA, Howarth CJ, Ibrahim A, Kolb FL, McMullen MS, Murphy JP, Ohm HW, Rossnagel BG, Yan WK, Miclaus KJ, Hiller J, Maughan PJ, Redman Hulse RR, Anderson JM, Islamovic E, Jackson EW (2013). SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One 8, e58068.
[36]	Oraby H, Ahmad R (2012). Physiological and biochemical changes of CBF3 transgenic oat in response to salinity stress. Plant Sci 185-186, 331-339.
[37]	Pawlowski WP, Somers DA (1998). Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA. Proc Natl Acad Sci USA 95, 12106-12110. PMID
[38]	Peng YY, Yan HH, Guo LC, Deng C, Wang CL, Wang YB, Kang LP, Zhou PP, Yu KQ, Dong XL, Liu XM, Sun ZY, Peng Y, Zhao J, Deng D, Xu YH, Li Y, Jiang QT, Li Y, Wei LM, Wang JR, Ma J, Hao M, Li W, Kang HY, Peng ZS, Liu DC, Jia JZ, Zheng YL, Ma T, Wei YM, Lu F, Ren CZ (2022). Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nat Genet 54, 1248-1258.
[39]	Somers DA, Rines HW, Gu WN, Kaeppler HF, Bushnell WR (1992). Fertile, transgenic oat plants. Biotechnology 10, 1589-1594.
[40]	Song GY, Huo PJ, Wu B, Zhang ZW (2015). A genetic linkage map of hexaploid naked oat constructed with SSR markers. Crop J 3, 353-357. DOI
[41]	Svitashev S, Ananiev E, Pawlowski WP, Somers DA (2000). Association of transgene integration sites with chromosome rearrangements in hexaploid oat. Theor Appl Genet 100, 872-880.
[42]	Tanhuanpää P, Kalendar R, Schulman AH, Kiviharju E (2008). The first doubled haploid linkage map for cultivated oat. Genome 51, 560-569. DOI PMID
[43]	Tanhuanpää P, Manninen O, Beattie A, Eckstein P, Scoles G, Rossnagel B, Kiviharju E (2012). An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials. Genome 55, 289-301. DOI PMID
[44]	Tinker NA, Kilian A, Wight CP, Heller-Uszynska K, Wenzl P, Rines HW, Bjørnstad Å, Howarth CJ, Jannink JL, Anderson JM, Rossnagel BG, Stuthman DD, Sorrells ME, Jackson EW, Tuvesson S, Kolb FL, Olsson O, Federizzi LC, Carson ML, Ohm HW, Molnar SJ, Scoles GJ, Eckstein PE, Bonman JM, Ceplitis A, Langdon T (2009). New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics 10, 39. DOI PMID
[45]	Tinker NA, Wight CP, Bekele WA, Yan WK, Jellen EN, Renhuldt NT, Sirijovski N, Lux T, Spannagl M, Mascher M (2022). Genome analysis in Avena sativa reveals hidden breeding barriers and opportunities for oat improvement. Commun Biol 5, 474.
[46]	Tumino G, Voorrips RE, Morcia C, Ghizzoni R, Germeier CU, Paulo MJ, Terzi V, Smulders MJM (2017). Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection. Euphytica 213, 163.
[47]	Yan HH, Bekele WA, Wight CP, Peng YY, Langdon T, Latta RG, Fu YB, Diederichsen A, Howarth CJ, Jellen EN, Boyle B, Wei YM, Tinker NA (2016). High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat. Theor Appl Genet 129, 2133-2149.
[48]	Zimmer CM, McNish IG, Esvelt Klos K, Eickholt DP, Arruda KMA, Pacheco MT, Smith KP, Federizzi LC (2021). Genome wide association mapping for kernel shape and its association with β-glucan content in oats. Crop Sci 61, 3986-3999.