Scanning for Pi Loci and Rebuilding an Improved Genome of Elite Rice Variety Kongyu 131

doi:10.11983/CBB16107

Abstract

Abstract: The rice variety Kongyu 131 (Oryza sativa ssp. japonica) is the most widely grown elite cultivar in Heilongjiang province because of its high quality, early maturity, high yield and cold resistance. However, because it has been cultivated in the same areas for many years, it is now highly susceptible to rice blast. By re-sequencing and scanning the whole genome of Kongyu 131, we found that it lacks more than 12 cloned blast resistance genes, including Pi2, Pi9, Pi36, Pi5-1, Pb1, Pid3, Pi25, Pikh, Pi1, Pik-m, Pik-p and Pi56t. To improve the blast resistance, we successfully introgressed Pb1 (Panicle blast 1) into Kongyu131. Without changing the other agronomic characters, we used 5 single nucleotide polymorphism markers to control the length of the introduced target fragment derived from the donor cultivar MP. Inoculating test results indicated that the improved line, containing a 700 kb target fragment and sharing 99.38% genetic background with Kongyu 131, showed the same blast resistance as MP.

Xiaohui Zhang, Xiaomin Feng, Shaoyang Lin. Scanning for Pi Loci and Rebuilding an Improved Genome of Elite Rice Variety Kongyu 131[J]. Chinese Bulletin of Botany, 2017, 52(1): 30-42.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.chinbullbotany.com/EN/10.11983/CBB16107

https://www.chinbullbotany.com/EN/Y2017/V52/I1/30

Figures/Tables 8

References 24

[1]	董志峰, 马荣才, 彭于发, 管华诗 (2001). 转基因植物中外源非目的基因片段的生物安全研究进展. 植物学报 43, 661-672.
[2]	姜玉英, 曾娟, 陆明红, 刘杰 (2013). 2013年全国主要粮食作物重大病虫害发生趋势预报. 植物保护 39, 1-4.
[3]	姜玉英, 曾娟, 陆明红, 刘杰 (2014). 2014年全国主要粮食作物重大病虫害发生趋势预报. 植物保护 40, 1-4.
[4]	姜玉英, 曾娟, 陆明红, 刘杰 (2015). 2015年全国三大谷类作物重大病虫害发生趋势预报. 植物保护 41, 1-4.
[5]	宋成艳, 王桂玲, 辛爱华, 丛万彪 (2007). 黑龙江省水稻品种空育131稻瘟病菌生理小种种类及发病原因分析. 黑龙江农业科学 (1), 41-42.
[6]	孙向东 (2005). 黑龙江省粮食主产区主要作物品种种植情况分析. 黑龙江农业科学 (2), 12-14.
[7]	Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, Mc- Adams SA, Faulk KN, Donaldson GK, Tarchini R, Valent B (2000). A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta.Plant Cell 12, 2033-2045.
[8]	Chen J, Shi Y, Liu W, Chai R, Fu Y, Zhuang J, Wu J (2011). A Pid3 allele from rice cultivar Gumei2 confers resistance to Magnaporthe oryzae.J Genetics Genomics 38, 209-216.
[9]	Chen X, Shang J, Chen D, Lei C, Zou Y, Zhai W, Liu G, Xu J, Ling Z, Cao G, Ma B, Wang Y, Zhao X, Li S, Zhu L (2006). A B-lectin receptor kinase gene conferring rice blast resistance.Plant J 46, 794-804.
[10]	Fukuoka S, Okuno K (2001). QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice.Theor Appl Genet 103, 185-190.
[11]	Hayashi N, Inoue H, Kato T, Funao T, Shirota M, Shimizu T, Kanamori H, Yamane H, Hayano-Saito Y, Matsumoto T, Yano M, Takatsuji H (2010). Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS- LRR protein and was generated by acquiring a promoter through local genome duplication.Plant J 64, 498-510.
[12]	Hua L, Wu J, Chen C, Wu W, He X, Lin F, Wang L, Ashikawa I, Matsumoto T, Wang L, Pan Q (2012). The isolation of Pi1, an allele at the Pik locus which confers broad spectrum resistance to rice blast.Theor Appl Genet 125, 1047-1055.
[13]	Inoue H, Hayashi N, Matsushita A, Liu X, Nakayama A, Sugano S, Jiang CJ, Takatsuji H (2013). Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY- 45 through protein-protein interaction.Proc Natl Acad Sci USA 110, 9577-9582.
[14]	Lin F, Chen S, Que Z, Wang L, Liu X, Pan Q (2007). The blast resistance gene Pi37 encodes a nucleotide binding site-leucine-rich repeat protein and is a member of a resistance gene cluster on rice chromosome 1.Genetics 177, 1871-1880.
[15]	Okuyama Y, Kanzaki H, Abe A, Yoshida K, Tamiru M, Saitoh H, Fujibe T, Matsumura H, Shenton M, Galam DC, Undan J, Ito A, Sone T, Terauchi R (2011). A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes.Plant J 66, 467-479.
[16]	Peleman JD, van der Voort JR (2003). Breeding by design.Trends Plant Sci 8, 330-334.
[17]	Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang GL (2006). The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172, 1901-1914.
[18]	Shang J, Tao Y, Chen X, Zou Y, Lei C, Wang J, Li X, Zhao X, Zhang M, Lu Z, Xu J, Cheng Z, Wan J, Zhu L (2009). Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site-leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes.Genetics 182, 1303-1311.
[19]	Takahashi A, Hayashi N, Miyao A, Hirochika H (2010). Unique features of the rice blast resistance Pish locus revealed by large scale retrotransposon-tagging. BMC Plant Biol 10,175.
[20]	Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing Y, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M (2008). The rice annotation project database (RAP-DB): 2008 update.Nucleic Acids Res 36, 1028-1033.
[21]	von Bubnoff A (2008). Next-generation sequencing: the race is on.Cell 132, 721-723.
[22]	Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L, Hayasaka H, Katayose Y, Sasaki T (1999). The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes.Plant J 19, 55-64.
[23]	Zhai C, Lin F, Dong Z, He X, Yuan B, Zeng X, Wang L, Pan Q (2011). The isolation and characterization of Pik, a rice blast resistance gene which emerged after rice domestication.New Phytol 189, 321-334.
[24]	Zhou B, Qu S, Liu G, Dolan M, Sakai H, Lu G, Bellizzi M, Wang GL (2006). The eight amino-acid differences within three Leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea.Mol Plant-Microbe Interact 19, 1216-1228.

Year	Artifical inoculation			Natural infection
Year	Seedling blast	Leaf blast	Panicle blast	Seedling blast	Leaf blast	Panicle blast
1995	8	8	9	6	5	9
1996	9	9	9	9	9	9
1998	unknown	9	9	unknown	9	9
1999	unknown	8	9	unknown	8	9
2002	unknown	9	9	unknown	8	9
2003	unknown	8	9	unknown	7	9
2004	unknown	7	9	unknown	7	7
2005	9	9	9	9	9	9

Year	Artifical inoculation			Natural infection
Year	Seedling blast	Leaf blast	Panicle blast	Seedling blast	Leaf blast	Panicle blast
1995	8	8	9	6	5	9
1996	9	9	9	9	9	9
1998	unknown	9	9	unknown	9	9
1999	unknown	8	9	unknown	8	9
2002	unknown	9	9	unknown	8	9
2003	unknown	8	9	unknown	7	9
2004	unknown	7	9	unknown	7	7
2005	9	9	9	9	9	9

Markers	Chr.		Position (IRGSP1.0)	Forward primer (5′-3′)	Reverse primer (5′-3′)
SNP1	11		24107429	CTTACAACCGAATTGCTTATCAC	TATAGGATAAGAGTCGAAAGCATC
SNP2	11		24552815	CCTCAACAGGATCCAGATTCAATAC	CAAGATCAATTGAGTTAGACAAC
SNP3		11	24717067	CCAGACATAATGCTTAAAGTAG	CATAGTCGCAGTTCATCTTATG
SNP4		11	24747927	GACATATTGTATGCAATCTACTCG	TTCACAGAAGCTAGTATAAGAG
SNP5	11		25104609	AAGTAATATACGCTACTATCTTG	CGACGTGATGGGTAAGAACAG

Markers	Chr.		Position (IRGSP1.0)	Forward primer (5′-3′)	Reverse primer (5′-3′)
SNP1	11		24107429	CTTACAACCGAATTGCTTATCAC	TATAGGATAAGAGTCGAAAGCATC
SNP2	11		24552815	CCTCAACAGGATCCAGATTCAATAC	CAAGATCAATTGAGTTAGACAAC
SNP3		11	24717067	CCAGACATAATGCTTAAAGTAG	CATAGTCGCAGTTCATCTTATG
SNP4		11	24747927	GACATATTGTATGCAATCTACTCG	TTCACAGAAGCTAGTATAAGAG
SNP5	11		25104609	AAGTAATATACGCTACTATCTTG	CGACGTGATGGGTAAGAACAG

Pi gene	Chr.	GenBank ID	BLAST results (with CDS)	Be contained or lacked in Kongyu 131
Pib	2	AB013448.1	High sequence homology	Uncertain
Pita/Pi4a	12	AF207842.1	3 SNP sites	Uncertain
Pi2/Piz5	6	DQ352453.1	53 SNP sites	Lacked
Pi9	6	DQ285630	Sequence deletion	Lacked
Pizt	6	DQ352040	High sequence homology	Uncertain
Pi36	8	DQ900896.1	Multi-SNP sites	Lacked
Pi37	1	DQ923494.1	4 SNP sites	Uncertain
Pi5-1/Pi3/Pii	9	EU869185.1	29 SNP sites	Lacked
Pit	1	AB379815.1	6 SNP sites	Uncertain
Pish	1	Os01g0782100	No difference	Contained
Pb1	11	AB570371.1	Structural variation	Lacked
Pia	11	AB604622 and AB604627	High sequence homology	Uncertain
pi-21	4	AB430853.1	1 SNP site	Uncertain
Pi-d2	6	FJ915121.1	6 SNP sites	Uncertain
Pi-d3	6	FJ773285	Terminator codon mutation	Lacked
Pi25	6	HM448480	18 SNP sites	Lacked
Pik	11	HM048900.1	2 SNP sites	Uncertain
Pikh/Pi-54	11	AY914077(Pikh)/HE589445 (Pi54)	Structural variation	Lacked
Pi1	11	HQ606329cds	11 SNP sites	Lacked
Pik-m	11	AB510262.1	Structural variation	Lacked
Pik-p	11	HM035360	Multi-SNP sites	Lacked
Pi56t	9	None	Multi-SNP sites	Lacked