Identification of New Allele of FLOURY ENDOSPERM2 in White-Core Endosperm Mutant of Rice

doi:10.1016/j.rsci.2022.07.003

Abstract

Bao Jinsong, Zhang Yu, Zhao Jiajia, Chen Yaling, Wu Weixun, Cao Liyong, Xu Feifei. Identification of New Allele of FLOURY ENDOSPERM2 in White-Core Endosperm Mutant of Rice[J]. Rice Science, 2022, 29(5): 407-411.

Figures/Tables 2

Fig. 1. One base pair deletion in FLO2 results in white-core endosperm mutant GM645. A, Schematic of bulked-segregant analysis (BSA) for detection of candidate genes for white-core endosperm (WE) in GM645. Twenty-six translucent endosperm (TE) lines and 26 WE lines selected from a recombinant inbred line (RIL)-F7 population were used for germination. Ten-day-old seedlings were used to extract genomic DNA individually, which was equally mixed to make the bulked TE DNA pool and WE DNA pool. Genomic DNA of the two bulked DNA pools, GM645 and Tainong 67 (TN67), were subjected for next generation sequencing. B, Absolute ΔSNP index plots for white-core endosperm. Absolute ΔSNP index = |SNP index WE pool - SNP index TE pool|. The significant peak (absolute ΔSNP index was around 1.0) was marked in the red cycle. C, Sanger sequencing and comparison of five candidate sites in four genes in Guanglu’ai 4 (GLA4), GM645 and TN67. D, Gene structure and mutation site of Os04g0645100. A thymine nucleotide deletion in GM645 causes premature termination of translation after 983 aa and has an additional 11 aa resulting from the frame shift mutation. The coding sequence for tetratricopeptide repeat domain is located in the red box. E, One base pair deletion in Os04g0645100 is associated with white-core endosperm in the RIL population. For the different lines, PCR products from WE-RIL are recognized and cut by the restriction enzyme Hinf І as GM645, while PCR products from TE-RIL cannot be cut by Hinf І as TN67.

Fig. 2. Complementary tests confirm that FLO2 largely rescues white-core endosperm to translucent in GM645. A, FLO2-3×HA-TurboID fusion protein express in GM645 transgenic plants (CL#1 to CL#5). Total protein was extracted from young grains at 10 d after flowering and analyzed the expression of the fusion protein by immunoblot with anti-HA antibody. B, Genetic complementation of FLO2 in GM645 rescues grain appearance. CL#1 and CL#2 mean complementary lines 1 and 2, respectively.

References 31

[1]	Bao J S. 2012. Towards understanding of the genetic and molecular basis of eating and cooking quality of rice. Cereal Food World, 57(4): 148-156.
[2]	Bello B K, Hou Y X, Zhao J, Jiao G A, Wu Y W, Li Z Y, Wang Y F, Tong X H, Wang W, Yuan W Y, Wei X J, Zhang J. 2019. NF-YB1-YC12-bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.). Plant Biotechnol J, 17(7): 1222-1235.
[3]	Cai Y, Zhang W W, Jin J, Yang X M, You X M, Yan H G, Wang L, Chen J, Xu J H, Chen W W, Chen X G, Ma J, Tang X J, Kong F, Zhu X P, Wang G X, Jiang L, Terzaghi W, Wang C M, Wan J M. 2018. OsPKpα1 encodes a plastidic pyruvate kinase that affects starch biosynthesis in the rice endosperm. J Integr Plant Biol, 60(11): 1097-1118.
[4]	Chen Y L, Pang Y H, Bao J S. 2020. Expression profiles and protein complexes of starch biosynthetic enzymes from white-core and waxy mutants induced from high amylose indica rice. Rice Sci, 27(2): 152-161.
[5]	Crofts N, Nakamura Y, Fujita N. 2017. Critical and speculative review of the roles of multi-protein complexes in starch biosynthesis in cereals. Plant Sci, 262: 1-8. PMID
[6]	Fu F F, Xue H W. 2010. Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol, 154(2): 927-938.
[7]	Hao Y Y, Wang Y L, Wu M M, Zhu X P, Teng X, Sun Y L, Zhu J P, Zhang Y Y, Jing R N, Lei J, Li J F, Bao X H, Wang C M, Wang Y H, Wan J M. 2019. The nuclear-localized PPR protein OsNPPR1 is important for mitochondrial function and endosperm development in rice. J Exp Bot, 70(18): 4705-4720. PMID
[8]	Kang H G, Park S, Matsuoka M, An G. 2005. White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C-type pyruvate orthophosphate dikinase gene (OsPPDKB). Plant J, 42(6): 901-911.
[9]	Kawagoe Y, Kubo A, Satoh H, Takaiwa F, Nakamura Y. 2005. Roles of isoamylase and ADP-glucose pyrophosphorylase in starch granule synthesis in rice endosperm. Plant J, 42(2): 164-174. PMID
[10]	Kong X L, Sun X, Xu F F, Umemoto T, Chen H, Bao J S. 2014. Morphological and physicochemical properties of two starch mutants induced from a high amylose indica rice by gamma irradiation. Starch Stärke, 66(1/2): 157-165.
[11]	Lei J, Teng X, Wang Y F, Jiang X K, Zhao H H, Zheng X M, Ren Y L, Dong H, Wang Y L, Duan E C, Zhang Y Y, Zhang W W, Yang H, Chen X L, Chen R B, Zhang Y, Yu M Z, Xu S B, Bao X H, Zhang P C, Liu S J, Liu X, Tian Y L, Jiang L, Wang Y H, Wan J M. 2022. Plastidic pyruvate dehydrogenase complex E1 component subunit Alpha1 is involved in galactolipid biosynthesis required for amyloplast development in rice. Plant Biotechnol J, 20(3): 437-453.
[12]	Long W H, Wang Y L, Zhu S S, Jing W, Wang Y H, Ren Y L, Tian Y L, Liu S J, Liu X, Chen L M, Wang D, Zhong M S, Zhang Y Y, Hu T T, Zhu J P, Hao Y Y, Zhu X P, Zhang W W, Wang C M, Zhang W H, Wan J M. 2018. FLOURY SHRUNKEN ENDOSPERM1 connects phospholipid metabolism and amyloplast development in rice. Plant Physiol, 177(2): 698-712.
[13]	Matsushima R, Maekawa M, Fujita N, Sakamoto W. 2010. A rapid, direct observation method to isolate mutants with defects in starch grain morphology in rice. Plant Cell Physiol, 51(5): 728-741. PMID
[14]	Nishi A, Nakamura Y, Tanaka N, Satoh H. 2001. Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. Plant Physiol, 127(2): 459-472. PMID
[15]	Pang Y H, Hu Y Q, Bao J S. 2021. Comparative phosphoproteomic analysis reveals the response of starch metabolism to high- temperature stress in rice endosperm. Int J Mol Sci, 22(19): 10546.
[16]	Peng C, Wang Y H, Liu F, Ren Y L, Zhou K N, Lv J, Zheng M, Zhao S L, Zhang L, Wang C M, Jiang L, Zhang X, Guo X P, Bao Y Q, Wan J M. 2014. FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice endosperm. Plant J, 77(6): 917-930.
[17]	She K C, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, Fukuda M, Naito N, Tsurumaki Y, Yaeshima M, Tsuge T, Matsumoto K, Kudoh M, Itoh E, Kikuchi S, Kishimoto N, Yazaki J, Ando T, Yano M, Aoyama T, Sasaki T, Satoh H, Shimada H. 2010. A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell, 22(10): 3280-3294.
[18]	Suzuki R, Imamura T, Nonaga Y, Kusano H, Teramura H, Sekine K T, Yamashita T, Shimada H. 2020. A novel FLOURY ENDOSPERM2 (FLO2)-interacting protein, is involved in maintaining fertility and seed quality in rice. Plant Biotechnol, 37(1): 47-55.
[19]	Tappiban P, Hu Y Q, Deng J M, Zhao J J, Ying Y N, Zhang Z W, Xu F F, Bao J S. 2022. Relative importance of branching enzyme isoforms in determining starch fine structure and physicochemical properties of indica rice. Plant Mol Biol, 108: 399-412.
[20]	Teng X, Zhong M S, Zhu X P, Wang C M, Ren Y L, Wang Y L, Zhang H, Jiang L, Wang D, Hao Y Y, Wu M M, Zhu J P, Zhang X, Guo X P, Wang Y H, Wan J M. 2019. FLOURY ENDOSPERM16 encoding a NAD-dependent cytosolic malate dehydrogenase plays an important role in starch synthesis and seed development in rice. Plant Biotechnol J, 17(10): 1914-1927.
[21]	Wang J C, Xu H, Zhu Y, Liu Q Q, Cai X L. 2013. OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm. J Exp Bot, 64(11): 3453-3466.
[22]	Wang R Q, Ren Y L, Yan H G, Teng X, Zhu X P, Wang Y P, Zhang X, Guo X P, Lin Q B, Cheng Z J, Lei C L, Wang J L, Jiang L, Wang Y H, Wan J M. 2021. ENLARGED STARCH GRAIN1 affects amyloplast development and starch biosynthesis in rice endosperm. Plant Sci, 305: 110831.
[23]	Wu M M, Ren Y L, Cai M H, Wang Y L, Zhu S S, Zhu J P, Hao Y Y, Teng X, Zhu X P, Jing R N, Zhang H, Zhong M S, Wang Y F, Lei C L, Zhang X, Guo X P, Cheng Z J, Lin Q B, Wang J, Jiang L, Bao Y Q, Wang Y H, Wan J M. 2019. Rice FLOURY ENDOSPERM10 encodes a pentatricopeptide repeat protein that is essential for the trans-splicing of mitochondrial nad1 intron 1 and endosperm development. New Phytol, 223(2): 736-750.
[24]	Xiong Y F, Ren Y, Li W, Wu F S, Yang W J, Huang X L, Yao J L. 2019. NF-YC12 is a key multi-functional regulator of accumulation of seed storage substances in rice. J Exp Bot, 70(15): 3765-3780. PMID
[25]	Xue M Y, Liu L L, Yu Y F, Zhu J P, Gao H, Wang Y H, Wan J M. 2019. Lose-of-function of a rice nucleolus-localized pentatricopeptide repeat protein is responsible for the floury endosperm14mutant phenotypes. Rice, 12(1): 100.
[26]	Yang X X, Wen Z Y, Zhang D L, Li Z, Li D W, Nagalakshmi U, Dinesh-Kumar S P, Zhang Y L. 2020. Proximity labeling: An emerging tool for probing in planta molecular interactions. Plant Commun, 2(2): 100137.
[27]	Yin L L, Xue H W. 2012. The MADS29 transcription factor regulates the degradation of the nucellus and the nucellar projection during rice seed development. Plant Cell, 24(3): 1049-1065.
[28]	You X M, Zhang W W, Hu J L, Jing R N, Cai Y, Feng Z M, Kong F, Zhang J, Yan H G, Chen W W, Chen X G, Ma J, Tang X J, Wang P, Zhu S S, Liu L L, Jiang L, Wan J M. 2019. FLOURY ENDOSPERM15 encodes a glyoxalase I involved in compound granule formation and starch synthesis in rice endosperm. Plant Cell Rep, 38(3): 345-359.
[29]	Yu M Z, Wu M M, Ren Y L, Wang Y H, Li J F, Lei C L, Sun Y L, Bao X H, Wu H M, Yang H, Pan T, Wang Y F, Jing R N, Yan M Y, Zhang H D, Zhao L, Zhao Z C, Zhang X, Guo X P, Cheng Z J, Yang B, Jiang L, Wan J M. 2021. Rice FLOURY ENDOSPERM 18encodes a pentatricopeptide repeat protein required for 5' processing of mitochondrial nad5 messenger RNA and endosperm development. J Integr Plant Biol, 63(5): 834-847.
[30]	Zhang J, Niu B X, E Z G, Chen C. 2021. Towards understanding the genetic regulations of endosperm development in rice. Chin J Rice Sci, 35(4): 326-341. (in Chinese with English abstract)
[31]	Zhou H J, Wang L J, Liu G F, Meng X B, Jing Y H, Shu X L, Kong X L, Sun J, Yu H, Smith S M, Wu D X, Li J Y. 2016. Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice. Proc Natl Acad Sci USA, 113(45): 12844-12849.