籼型血缘渗入对北方粳稻产量和品质的影响

doi:10.3864/j.issn.0578-1752.2023.22.001

摘要/Abstract

摘要：

【目的】分析籼型血缘渗入对粳稻品种产量和品质的影响，为优化籼型血缘利用的北方粳稻育种方案提供理论基础和基因组资源。【方法】以籼粳交重组自交系（RIL）及从黑龙江省、辽宁省、山东省和江苏省收集的74份不同年代粳稻主栽品种为试材，结合基于Illumina HiSeq2500平台的全基因组高通量测序和多地表型调查，分析籼型血缘对北方粳稻产量和品质的影响，并使用CRISPR/Cas9基因编辑技术对籼型血缘渗入所引入的不利基因进行基因敲除。【结果】分析RIL发现籼型血缘与穗长、粒长呈显著正相关，与碾磨品质呈负相关，其中，与整精米率达到显著水平。籼型血缘在江苏省与直链淀粉含量呈显著负相关，与粗蛋白含量呈显著正相关。籼型频率与粒形的相关性随着纬度的增加而增强，而与穗长和整精米率的相关性随着纬度的增加而减弱。通过调查粳稻主要稻区不同年代主栽品种，发现籼型血缘渗入位置和比例并不是均匀分布在12条染色体上，在第1、10、11和12染色体上，籼型血缘分布较多。江苏省和辽宁省主栽品种的籼型血缘显著高于黑龙江省和山东省，而且2000年后育成的品种籼型血缘显著高于2000年之前的品种。各粳稻区不同年代主栽品种籼型血缘渗入显著增加了每穗粒数，籼型血缘渗入区域中包含多个抗性和育性相关基因。在盐丰47的第5染色体上有一段籼型血缘渗入片段，包含籼型粒型调控基因GS5和籼型垩白调控基因Chalk5，增加了盐丰47的千粒重，但影响了其垩白性状。应用CRISPR/Cas9技术敲除盐丰47的Chalk5，纯合基因编辑植株的粒形与盐丰47相似，其垩白性状得到了显著改善。【结论】籼型血缘渗入主要通过增加每穗粒数增加粳稻产量潜力，但对碾磨品质有负面影响。通过全基因组高通量测序挖掘品种不良等位基因，结合CRISPR/Cas9基因编辑打破籼粳杂交育种中的遗传累赘是一种高效的育种辅助手段，可以针对目标性状进行快速准确的改良。

关键词: 水稻, 粳稻育种, 籼型血缘渗入, 产量, 品质, 分子设计育种

Abstract:

【Objective】To demonstrate the impact of indica/Xian (XI) pedigree introgression on the yield and quality of japonica/Geng (GJ) rice varieties, providing a theoretical basis and genomic resources for optimizing XI pedigree introgression breeding programs in northern GJ rice.【Method】In this study, the whole genome sequence on Illumina platform was employed to elucidate the effects of XI pedigree introgression on the yield and quality of rice in Northeast China were analyzed using recombinant inbred lines (RIL) derived from the cross between XI and GJ varieties, and 74 major GJ varieties grown from Heilongjiang, Liaoning, Shandong, and Jiangsu provinces as test materials. Using CRISPR/Cas9 gene editing technology to knock out the unfavorable genes introduced by XI pedigree introgression. 【Result】Analysis of RIL revealed a significant positive correlation between XI pedigree introgression and panicle length, grain length, and a negative correlation with head rice ratio. XI pedigree introgression was significantly negatively correlated with Amylose content, and significantly positively correlated with protein content in Jiangsu. With the increase of latitude, the correlation efficiency between XI pedigree introgression and grain shape increased, while the correlation between XI pedigree introgression and panicle length and head rice ratio decreased. The genomic fragments of XI pedigree introgression are unevenly distributed across different chromosomes and are more abundantly present on chromosomes 1, 10, 11, and 12. The XI pedigree introgression of the major cultivars in Jiangsu and Liaoning provinces is significantly higher than that in Heilongjiang and Shandong provinces, and the XI pedigree introgression of the cultivars after 2000 is significantly higher than that before 2000. The XI pedigree introgression includes multiple resistance and fertility-related genes. The project identified an XI pedigree introgression fragment on chromosome 5 of YF47, including the XI type grain regulatory gene GS5 and XI type chalkiness regulatory gene Chalk5, which increased the 1000 grain weight of YF47 but affected its chalkiness-related traits. The project uses CRISPR/Cas9 technology to knock out the Chalk5 gene of YF47. The grain shape of the homozygous gene editing plants is similar to those of YF47, and its chalkiness character has been significantly improved. 【Conclusion】The XI pedigree introgression mainly increases the yield potential of GJ rice by increasing the number of grains per panicle, but has a negative impact on milling quality. Exploring the unfavorable alleles in varieties through high-throughput genome sequencing, combined with CRISPR/Cas9 gene editing, to break the genetic drag in breeding using the cross between XI and GJ, is an efficient breeding strategy that can quickly and accurately improve target traits.

Key words: rice, japonica/Geng breeding, indica/Xian pedigree introgression, yield, quality, molecular design breeding

徐海, 李秀坤, 芦佳浩, 姜恺, 马玥, 徐正进, 徐铨. 籼型血缘渗入对北方粳稻产量和品质的影响[J]. 中国农业科学, 2023, 56(22): 4359-4370.

XU HAI, LI XIUKUN, LU JIAHAO, JIANG KAI, MA YUE, XU ZHENGJIN, XU QUAN. The Effect of indica/Xian Pedigree Introgression in japonica/Geng Rice Breeding in China[J]. Scientia Agricultura Sinica, 2023, 56(22): 4359-4370.

图/表 5

图1

图2

图3

图4

图5

参考文献 42

[1]	GARRIS A J, TAI T H, COBURN J, KRESOVICH S, MCCOUCH S. Genetic structure and diversity in Oryza sativa L.. Genetics, 2005, 169(3): 1631-1638. doi: 10.1534/genetics.104.035642
[2]	Huang X H, WEI X H, SANG T, ZHAO Q, FENG Q, ZHAO Y, LI C Y, ZHU C R, LU T T, ZHANG Z W, LI M, FAN D L, GUO Y L, WANG A H, WANG L, DENG L W, LI W J, LU Y Q, WENG Q J, LIU K Y, HUANG T, ZHOU T Y, JING Y F, LI W, LIN Z, BUCKLER E S, QIAN Q, ZHANG Q F, LI J Y, HAN B. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 2010, 42(11): 961-967. doi: 10.1038/ng.695 pmid: 20972439
[3]	Huang X H, ZHAO Y, WEI X H, LI C Y, WANG A H, ZHAO Q, LI W J, GUO Y L, DENG L W, ZHU C R, FAN D L, LU Y Q, WENG Q J, LIU K Y, ZHOU T Y, JING Y F, SI L Z, DONG G J, HUANG T, LU T T, FENG Q, QIAN Q, LI J Y, HAN B. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics, 2012, 44(1): 32-39. doi: 10.1038/ng.1018
[4]	Yu H, Lin T, Meng X B, DU H L, ZHANG J K, LIU G F, CHEN M J, JING Y H, KOU L Q, LI X X, GAO Q, LIANG Y, LIU X D, FAN Z L, LIANG Y T, CHENG Z K, CHEN M S, TIAN Z X, WANG Y H, CHU C C, LI J Y. A route to de novo domestication of wild allotetraploid rice. Cell, 2021, 184(5): 1156-1170. e14. doi: 10.1016/j.cell.2021.01.013
[5]	Wang W S, MAULEON R, HU Z Q, CHEBOTAROV D, TAI S S, WU Z C, LI M, ZHENG T Q, FUENTES R R, ZHANG F, MANSUETO L, COPETTI D, SANCIANGCO M, PALIS K C, XU J L, SUN C, FU B Y, ZHANG H L, GAO Y M, ZHAO X Q, SHEN F, CUI X, YU H, LI Z C, CHEN M L, DETRAS J, ZHOU Y L, ZHANG X Y, ZHAO Y, KUDRNA D, WANG C C, LI R, JIA B, LU J Y, HE X C, DONG Z T, XU J B, LI Y H, WANG M, SHI J X, LI J, ZHANG D B, LEE S, HU W S, POLIAKOV A, DUBCHAK I, ULAT V J, BORJA F N, MENDOZA J R, ALI J, LI J, GAO Q, NIU Y C, YUE Z, NAREDO M E B, TALAG J, WANG X Q, LI J J, FANG X D, YIN Y, GLASZMANN J C, ZHANG J W, LI J Y, HAMILTON R S, WING R A, RUAN J, ZHANG G Y, WEI C C, ALEXANDROV N, MCNALLY K L, LI Z K, LEUNG H. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 2018, 557(7703): 43-49. doi: 10.1038/s41586-018-0063-9
[6]	WEI X, QIU J, YONG K C, FAN J J, ZHANG Q, HUA H, LIU J, WANG Q, OLSEN K M, HAN B, HUANG X H. A quantitative genomics map of rice provides genetic insights and guides breeding. Nature Genetics, 2021, 53(2): 243-253. doi: 10.1038/s41588-020-00769-9 pmid: 33526925
[7]	Liu Y Q, WANG H R, JIANG Z M, WANG W, XU R N, WANG Q H, ZHANG Z H, LI A F, LIANG Y, OU S J, LIU X J, CAO S Y, TONG H N, WANG Y H, ZHOU F, LIAO H, HU B, CHU C C. Genomic basis of geographical adaptation to soil nitrogen in rice. Nature, 2021, 590(7847): 600-605. doi: 10.1038/s41586-020-03091-w
[8]	ZHOU G, CHEN Y, YAO W, ZHANG C J, XIE W B, HUA J P, XING Y Z, XIAO J H, ZHANG Q F. Genetic composition of yield heterosis in an elite rice hybrid. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(39): 15847-15852.
[9]	杨守仁, 赵纪书. 籼粳稻杂交问题之研究. 农业学报, 1959, 10 (4): 256-268.
	YANG S R, ZHAO J S. A study on the problem of cross between XI and GJ rice. Acta Agriculture Sinica, 1959, 10(4): 256-268. (in Chinese)
[10]	徐正进, 陈温福. 中国北方粳型超级稻研究进展. 中国农业科学, 2016, 49(2): 239-250. doi: 10.3864/j.issn.0578-1752.2016.02.005
	XU Z J, CHEN W F. Research progress and related problems on japonica super rice in northern China. Scientia Agricultura Sinica, 2016, 49(2): 239-250. (in Chinese)
[11]	徐铨, 唐亮, 徐凡, 福嶌阳, 黄瑞冬, 陈温福, 徐正进. 粳稻食味品质改良研究现状与展望. 作物学报, 2013, 39(6): 961-968.
	XU Q, TANG L, XU F, FU D Y, HUANG R D, CHEN W F, XU Z J. Research advances and prospects of eating and quality improvement in Japonica rice (Oryza sativa L.) Acta Agronomica Sinica, 2013, 39(6): 961-968. (in Chinese) doi: 10.3724/SP.J.1006.2013.00961
[12]	LI X K, WU L, WANG J H, SUN J, XIA X H, GENG X, WANG X H, XU Z J, XU Q. Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality- associated loci. BMC Biology, 2018, 16(1): 102. doi: 10.1186/s12915-018-0572-x
[13]	Ashikari M, Sakakibara H, Lin S Y, YAMAMOTO T, TAKASHI T, NISHIMURA A, ANGELES E R, QIAN Q, KITANO H, MATSUOKA M. Cytokinin oxidase regulates rice grain production. Science, 2005, 309(5735): 741-745. doi: 10.1126/science.1113373 pmid: 15976269
[14]	Wang Y, Li F c, Zhang F, WU L, XU N, SUN Q, CHEN H, YU Z W, LU J H, JIANG K, WANG X C, WEN S Y, ZHOU Y, ZHAO H, JIANG Q, WANG J H, JIA R Z, SUN J, TANG L, XU H, HU W, XU Z J, CHEN W F, GUO A P, XU Q. Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding. Plant Biotechnology Journal, 2023, 21(1): 202-218. doi: 10.1111/pbi.v21.1
[15]	ZHANG F, XUE H Z, DONG X R, LI M, ZHENG X M, LI Z K, XU J L, WANG W S, WEI C C. Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes. Genome Research, 2022, 32(5): 853-863. doi: 10.1101/gr.276015.121 pmid: 35396275
[16]	Qin P, Lu H W, DU H L, WANG H, CHEN W L, CHEN Z, HE Q, OU S J, ZHANG H Y, LI X Z, LI X X, LI Y, LIAO Y, GAO Q, TU B, YUAN H, MA B T, WANG Y P, QIAN Y W, FAN S J, LI S G. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell, 2021, 184(13): 3542-3558. e16. doi: 10.1016/j.cell.2021.04.046 pmid: 34051138
[17]	GHOSH A, PAREEK A, SOPORY S K, SINGLA-PAREEK S L. A glutathione responsive rice glyoxalase II, OsGLYII-2, functions in salinity adaptation by maintaining better photosynthesis efficiency and anti-oxidant pool. The Plant Journal, 2014, 80(1): 93-105. doi: 10.1111/tpj.12621 pmid: 25039836
[18]	DU H, WANG N L, CUI F, LI X H, XIAO J H, XIONG L Z. Characterization of the beta-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice. Plant Physiology, 2010, 154(3): 1304-1318. doi: 10.1104/pp.110.163741 pmid: 20852032
[19]	ZOU J, LIU A L, CHEN X B, ZHOU X Y, GAO G F, WANG W F, ZHANG X W. Expression analysis of nine rice heat shock protein genes under abiotic stresses and ABA treatment. Journal of Plant Physiology, 2009, 166(8): 851-861. doi: 10.1016/j.jplph.2008.11.007 pmid: 19135278
[20]	ZHOU L Y, NI E D, YANG J W, ZHOU H, LIANG H, LI J, JIANG D G, WANG Z H, LIU Z L, ZHUANG C X. Rice OsGL1-6 is involved in leaf cuticular wax accumulation and drought resistance. PLoS ONE, 2013, 8(5): e65139. doi: 10.1371/journal.pone.0065139
[21]	Liu Y q, Wu H, Chen H, LIU Y L, HE J, KANG H Y, SUN Z G, PAN G, WANG Q, HU J L, ZHOU F, ZHOU K N, ZHENG X M, REN Y L, CHEN L M, WANG Y H, ZHAO Z G, LIN Q B, WU F Q, ZHANG X, GUO X P, CHENG X N, JIANG L, WU C Y, WANG H Y, WAN J M. A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice. Nature Biotechnology, 2015, 33(3): 301-305. doi: 10.1038/nbt.3069 pmid: 25485617
[22]	Zhao H J, WANG X Y, JIA Y L, MINKENBERG B, WHEATLEY M, FAN J B, JIA M H, FAMOSO A, EDWARDS J D, WAMISHE Y, VALENT B, WANG G L, YANG Y N. The rice blast resistance gene Ptr encodes an atypical protein required for broad-spectrum disease resistance. Nature Communications, 2018, 9: 2039. doi: 10.1038/s41467-018-04369-4 pmid: 29795191
[23]	Zhou H, Zhou M, Yang Y Z, LI J, ZHU L Y, JIANG D G, DONG J F, LIU Q J, GU L F, ZHOU L Y, FENG M J, QIN P, HU X C, SONG C L, SHI J F, SONG X W, NI E D, WU X J, DENG Q Y, LIU Z L, CHEN M S, LIU Y G, CAO X F, ZHUANG C X. RNaseZ^S1 processes Ub_L40 mRNAs and controls thermosensitive genic male sterility in rice. Nature Communications, 2014, 5: 4884. doi: 10.1038/ncomms5884 pmid: 25208476
[24]	Zhang P P, ZHANG Y X, SUN L P, SINUMPORN S, YANG Z F, SUN B, XUAN D D, LI Z H, YU P, WU W X, WANG K J, CAO L Y, CHENG S H. The rice AAA-ATPase OsFIGNL1 is essential for male meiosis. Frontiers in Plant Science, 2017, 8: 1639. doi: 10.3389/fpls.2017.01639 pmid: 29021797
[25]	SONG S Y, CHEN Y, LIU L, SEE Y H B, MAO C Z, GAN Y B, YU H. OsFTIP7 determines auxin-mediated anther dehiscence in rice. Nature Plants, 2018, 4(7): 495-504. doi: 10.1038/s41477-018-0175-0 pmid: 29915329
[26]	ZHOU L J, XIAO L T, XUE H W. Dynamic cytology and transcriptional regulation of rice Lamina joint development. Plant Physiology, 2017, 174(3): 1728-1746. doi: 10.1104/pp.17.00413
[27]	ZHANG J, FAN X W, HU Y, ZHOU X C, HE Q, LIANG L W, XING Y Z. Global analysis of CCT family knockout mutants identifies four genes involved in regulating heading date in rice. Journal of Integrative Plant Biology, 2021, 63(5): 913-923. doi: 10.1111/jipb.13013
[28]	LI Y B, FAN C C, XING Y Z, JIANG Y H, LUO L J, SUN L, SHAO D, XU C J, LI X H, XIAO J H, HE Y Q, ZHANG Q F. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 2011, 43(12): 1266-1269. doi: 10.1038/ng.977 pmid: 22019783
[29]	LI Y B, FAN C C, XING Y Z, YUN P, LUO L J, YAN B, PENG B, XIE W B, WANG G W, LI X H, XIAO J H, XU C G, HE Y Q. Chalk5 encodes a vacuolar H⁺-translocating pyrophosphatase influencing grain chalkiness in rice. Nature Genetics, 2014, 46(4): 398-404. doi: 10.1038/ng.2923
[30]	Huang X h, Kurata N, Wei X H, WANG Z X, WANG A H, ZHAO Q, ZHAO Y, LIU K Y, LU H Y, LI W J, GUO Y L, LU Y Q, ZHOU C C, FAN D L, WENG Q J, ZHU C R, HUANG T, ZHANG L, WANG Y C, FENG L, FURUUMI H, KUBO T, MIYABAYASHI T, YUAN X P, XU Q, DONG G J, ZHAN Q L, LI C Y, FUJIYAMA A, TOYODA A, LU T T, FENG Q, QIAN Q, LI J Y, HAN B. A map of rice genome variation reveals the origin of cultivated rice. Nature, 2012, 490(7421): 497-501. doi: 10.1038/nature11532
[31]	Xie W B, WANG G W, YUAN M, YAO W, LYU K, ZHAO H, YANG M, LI P B, ZHANG X, YUAN J, WANG Q X, LIU F, DONG H X, ZHANG L J, LI X L, MENG X Z, ZHANG W, XIONG L Z, HE Y Q, WANG S P, YU S B, XU C G, LUO J, LI X H, XIAO J H, LIAN X M, ZHANG Q F. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(39): E5411-E5419.
[32]	Zhao K Y, TUNG C W, EIZENGA G C, WRIGHT M H, ALI M L, PRICE A H, NORTON G J, ISLAM M R, REYNOLDS A, MEZEY J, MCCLUNG A M, BUSTAMANTE C D, MCCOUCH S R. Genome- wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications, 2011, 2: 467. doi: 10.1038/ncomms1467
[33]	CUI D, ZHOU H, MA X D, LIN Z C, SUN L H, HAN B, LI M M, SUN J C, LIU J, JIN G X, WANG X J, CAO G L, DENG X W, HE H, HAN L Z. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. Plant Communication, 2022, 3(3): 100325. doi: 10.1016/j.xplc.2022.100325
[34]	Chen Z, Bu Q Y, LIU G F, WANG M Q, WANG H R, LIU H Z, LI X F, LI H, FANG J, LIANG Y, TENG Z F, KANG S, YU H, CHENG Z K, XUE Y B, LIANG C Z, TANG J Y, LI J Y, CHU C C. Genomic decoding of breeding history to guide breeding-by-design in rice. National Science Review, 2023, 10(5): nwad029. doi: 10.1093/nsr/nwad029
[35]	FEI C, XU Q, XU Z J, CHEN W F. Effect of rice breeding process on improvement of yield and quality in China. Rice Science, 2020, 27(5): 363-367. doi: 10.1016/j.rsci.2019.12.009
[36]	SHAN Q W, WANG Y P, LI J, ZHANG Y, CHEN K L, LIANG Z, ZHANG K, LIU J X, XI J J, QIU J L, GAO C X. Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology, 2013, 31(8): 686-688. doi: 10.1038/nbt.2650 pmid: 23929338
[37]	CUI Y, ZHU M M, XU Z J, XU Q. Assessment of the effect of ten heading time genes on reproductive transition and yield components in rice using a CRISPR/Cas9 system. Theoretical and Applied Genetics, 2019, 132(6): 1887-1896. doi: 10.1007/s00122-019-03324-1 pmid: 30887096
[38]	CUI Y, JIANG N, XU Z J, XU Q. Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice. BMC Plant Biology, 2020, 20(1): 90. doi: 10.1186/s12870-020-2289-6 pmid: 32111163
[39]	LU Y M, YE X, GUO R M, HUANG J, WANG W, TANG J Y, TAN L T, ZHU J K, CHU C C, QIAN Y W. Genome-wide targeted mutagenesis in rice using the CRISPR/Cas9 system. Molecular Plant, 2017, 10(9): 1242-1245. doi: S1674-2052(17)30173-9 pmid: 28645638
[40]	ZENG D C, LIU T L, MA X L, WANG B, ZHENG Z Y, ZHANG Y L, XIE X R, YANG B W, ZHAO Z, ZHU Q L, LIU Y G. Quantitative regulation of Waxy expression by CRISPR/Cas9-based promoter and 5'UTR-intron editing improves grain quality in rice. Plant Biotechnology Journal, 2020, 18(12): 2385-2387. doi: 10.1111/pbi.v18.12
[41]	HUANG L C, LI Q F, ZHANG C Q, CHU R, GU Z W, TAN H Y, ZHAO D S, FAN X L, LIU Q Q. Creating novel Wx alleles with fine-tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR/Cas9 system. Plant Biotechnology Journal, 2020, 18(11): 2164-2166. doi: 10.1111/pbi.v18.11
[42]	SONG X G, MENG X B, GUO H Y, CHENG Q, JING Y H, CHEN M J, LIU G F, WANG B, WANG Y H, LI J Y, YU H. Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size. Nature Biotechnology, 2022, 40(9): 1403-1411. doi: 10.1038/s41587-022-01281-7 pmid: 35449414