Genetic Analysis of Plant Height and Allelic Variation of SD1 in Oryza glumaepatula

doi:10.7668/hbnxb.20194324

Abstract

Abstract:

In order to investigate the reasons for the differences in plant height between SSSL-B50 and HJX74,an F₂ population was constructed by backcrossing SSSL-B50 with HJX74 for genetic analysis and gene mapping of the plant.The genetic analysis showed that F₁ plants exhibited tall plant height.And the separation ratio within F₂ was 3:1(χ²=0.18<3.84)between the tall plant individuals and the semi-dwarf ones,which indicated that the tall plant height of SSSL-B50 was a dominant trait.Based on the linkage analysis between the marker genotypes and phenotypes of plant height in the F₂ population,the gene controlling tall plant height was mapped between markers S18 and X161 within the 38.38—39.07 Mb interval of the substituted segment on chromosome 1.Moreover,it was found that the known gene of "Green revolution",SD1,fell to the mapping interval.Through amplification and sequence alignment of SD1 gene in Oryza glumaepatula,SSSL-B50,and HJX74,it showed that a 280 bp deletion in CDS in HJX74 compared with Oryza glumaepatula and SSSL-B50.The qRT-PCR results showed that the expression level of SD1 was significantly higher in the second,third,and fourth sections of SSSL-B50 stem than in HJX74.The comparison of the SD1 gene sequence of Oryza glumaepatula with the previous reported results showed that the base substitutions occurred at two sites (E100G, Q339R) in the encoded amino acid.The results revealed that the tall plant height of SSSL-B50 was controlled by SD1.Furthermore,a new allelic type of SD1, SD1^Glu,was identified in Oryza glumaepatula.

Key words: Oryza glumaepatula, Plant height, Single segment substitution line, Gene mapping, Allelic type

YANG Xiandong, LIU Wei, CAO Lixia, LI Xiaohui, LU Yi, FU Xuelin. Genetic Analysis of Plant Height and Allelic Variation of SD1 in Oryza glumaepatula[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(1): 18-26. doi: 10.7668/hbnxb.20194324.

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Figures/Tables 8

Tab.1 Primers used in this experiment

引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')	用途 Purpose
RM486-F	CCCCCCTCTCTCTCTCTCTC	定位
RM486-R	TAGCCACATCAACAGCTTGC	定位
S18-F	CTAAATGAGACTAATTTGG	定位
S18-R	CTGTTCCAATCACAAACAATGG	定位
X161-F	GTATTGAATTGTTTCGGG	定位
X161-R	GAATTGCGATGAAGAGATAG	定位
X197-F	GTCCAAACTCTTCCATGAAG	定位
X197-R	GATCGACCATGACTGCTCT	定位
PSM369-F	GAGCCACTGATGCACCGAA	定位
PSM369-R	CGCCACCTTCACCTTCTTGT	定位
S1-F	GCGTCACGTAATGGATGGAGTATTATACAACACC	克隆SD1基因
S1-R	GTTAGGAGTAGCTCTGATGTAGATAAGCC	克隆SD1基因
SD2-F	TGTGCGACCTGAGGATGGAG	qRT-PCR
SD2-R	ACGTCGACCACGGGCATGTCCAG	qRT-PCR

Fig.1 Comparison of plant types and plant heights among the tested materials B. Comparision of the average plant height among the materials in 2020—2022; in which the plant height value of F₁ was the average of 10 individual plants in the late season of 2020.Different capital letters represented the significant differences at P<0.001. The same as Fig.2,6,7.

Fig.2 The distribution of plant height in F₂ population A.Distribution frequency of the plant height in F₂ population; B. Number of the individual plants in different genotype; C. Average plant height of three genotypes in F₂.

Fig.3 The linkage map of the gene for tall plant height in SSSL-B50

Fig.4 Variations of SD1 in HJX74 and Oryza glumaepatula(Glu) and the alignment of the encoded amino acid sequences A. Variations of SD1 in HJX74 and Oryza glumaepatula gene:the black filled boxes. Exons;White boxes. Introns;The gray filled boxes. 5'UTR and 3'UTR;△ and ▽. Base deletions and insertions in HJX74 compared with Oryza glumaepatula, respectively.B.Alignment of the amino acid sequences encoded by SD1 between HJX74 and Oryza glumaepatula.

Fig.5 Differences in amino acid sequences encoded by SD1 genes in different rice germplasms NIP, TC65, and Glu represented Nipponhare, Taichung 65, and Oryza glumaepatula, respectively.

Fig.6 Comparison of the internodal lengths between HJX74 and SSSL-B50,and the relative expression levels of SD1 in the internodes A.HJX74 and SSSL-B50 internode elongation pattern diagram; B, C.The internode length of HJX74 and SSSL-B50 at different growth stages; Ⅰ—Ⅵ indicated the first to the sixth internode; D. Relative expression levels of SD1 in the internodes of HJX74 and SSSL-B50 during booting stage. Different lowercase letters represented the significant differences at P<0.05.

Fig.7 Plant height of HJX74 under the condition of external GA₃ application

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