Fine Mapping of QTLs for Stigma Exsertion Rate from Oryza glaberrima by Chromosome Segment Substitution

doi:10.1016/j.rsci.2021.12.005

Abstract

Abstract:

Stigma exsertion is an important trait for outcrossing ability in rice. Stigma exsertion rate (SER) of male sterile lines (MSLs) is a key factor affecting F₁-seed production in hybrid rice. In this study, seven QTLs for SER were detected on five chromosomes using a set of single-segment substitution lines (SSSLs) derived from O. glaberrima. Three of the QTLs were mapped in the estimated intervals of 92.5-333.0 kb. qSER-5 was located in a substitution segment of 92.5 kb. qSER-1b and qSER-8b were respectively limited to 333.0 kb and 107.5 kb by secondary substitution mapping. qSER-1b and qSER-3 had bigger additive effects of 11.5% and 11.9%, respectively, while the other five QTLs had smaller additive effects from 5.7% to 8.6%. Open reading frames were identified in the regions of qSER-5 and qSER-8b in O. sativa and O. glaberrima genomes. Fine mapping of the QTLs laid a foundation for the cloning of genes, and QTLs for SER will be used to develop MSLs with strong ability of outcrossing.

Key words: stigma exsertion, QTL, single-segment substitution line, substitution mapping, Oryza glaberrima

Tan Quanya, Zhu Haitao, Liu Hui, Ni Yuerong, Wu Shengze, Luan Xin, Liu Junwei, Yang Weifeng, Yang Zifeng, Zeng Ruizhen, Liu Guifu, Wang Shaokui, Zhang Guiquan. Fine Mapping of QTLs for Stigma Exsertion Rate from Oryza glaberrima by Chromosome Segment Substitution[J]. Rice Science, 2022, 29(1): 55-66.

Figures/Tables 6

Fig. 1. Stigma exsertion rate (SER) of single-segment substitution lines (SSSLs) and their parents. A, Exserted stigmas in the panicles of parents. Red arrows point the exserted stigmas. Scale bars are 1 cm. B, Stigma exsertion rates of SSSLs and their donors. Huajingxian 74 (HJX74) was used as a control. ***, P ≤ ?0.001. C, Comparison of SER between the first cropping season (FCS) and the second cropping season (SCS) in seven SSSLs. Data in B and C are Mean ± SE (n = 3).

Fig. 2. Secondary substitution mapping of qSER-1b. A, Plant type of Huajingxian 74 (HJX74), HPS11 and HPS11-1. Scale bar is 15 cm. B, Substitution segment on chromosome 1 in HPS11. Physical distance (Mb) is shown under the chromosome. C, Substitution segments of HPS11-1 and HPS11-2. The position of Sd1 is pointed by the triangle (Sasaki et al, 2002). D, Stigma exsertion rate (SER) in HJX74, HPS11, HPS11-1 and HPS11-2. E, Plant height of HJX74, HPS11, HPS11-1 and HPS11-2. F, Secondary substitution mapping of qSER-1b based on the substitution segment of HPS11-1. G, Secondary substitution mapping of qSER-1b based on the substitution segment of HPS11-1-132. H, SER effects of three genotypes of qSER-1b in an F2 population. aa, Homozygous genotype of HJX74; Aa, Heterozygous genotype of HPS11-1/HJX74; AA, Homozygous genotype of HPS11-1. White and black blocks on chromosomes represent the genotypes of HJX74 and donor, respectively. Data in D-H are Mean ± SE (n = 3). Different uppercase letters above the bars indicate significant difference at the 0.001 level.

Fig. 3. Secondary substitution mapping of qSER-8b. A, Substitution segment on chromosome 8 in HPS14. Physical distance (Mb) is shown under the chromosome. B, Plant type of Huajingxian 74 (HJX74) and HPS14. Scale bar, 15 cm. C, Secondary substitution mapping based on the substitution segment of HPS14. D, Secondary substitution mapping of qSER-8b based on the substitution segment of HPS14-19. E, Stigma exsertion rate (SER) effects of three genotypes of qSER-8b in an F2 population. aa, Homozygous genotype of HJX74; Aa, Heterozygous genotype of HPS14/HJX74; AA, Homozygous genotype of HPS14. Data in C-E are Mean ± SE (n = 3). Different uppercase letters above bars indicate significant difference at the 0.001 level.

Fig. 4. Chromosomal locations of the seven QTLs of SER in single-segment substitution lines. Black bars on the right of each chromosome were the estimated intervals of QTLs with their names on the right. SER, Stigma exsertion rate; Chr., Chromosome; Mb, Megabase.

Table 1. Additive effects of QTLs for stigma exsertion rate (SER) detected in single-segment substitution lines.

QTL	Chromosome	Interval (kb)	Estimated length (kb)	Maximum length (kb)	Additive effect (%)
qSER-1a	1	12 291.6-19 797.0	7 505.4	8 302.9	8.0 ± 0.7
qSER-1b	1	25 759.6-26 092.6	333.0	500.2	11.5 ± 1.0
qSER-3	3	16 161.4-17 105.0	943.5	965.1	11.9 ± 1.1
qSER-5	5	3 448.9-3 541.4	92.5	104.0	8.6 ± 0.6
qSER-8a	8	2 685.9-5 716.0	3 030.1	3 360.3	5.7 ± 0.5
qSER-8b	8	27 510.3-27 617.8	107.5	152.5	8.0 ± 0.7
qSER-12	12	25 351.7-26 992.7	1 641.0	1 980.5	6.5 ± 0.6

Fig. 5. Maximum intervals and numbers of open reading frames (ORFs) of qSER-5 and qSER-8b in genomes of O. sativa and O. glaberrima. A, Maximum interval of qSER-5 on chromosome 5 of the two genomes. B, Number of ORFs of the qSER-5 interval identified in the two genomes. C, Maximum interval of qSER-8b on chromosome 8 of the two genomes. D, Number of ORFs of the qSER-8b interval identified in the two genomes. In A and C, white and black blocks represent respectively the chromosome segments of O. sativa and O. glaberrima. In B and D, the number in the shaded box is the number of ORFs identified in the O. sativa and O. glaberrima genomes, whereas the number in the gray box is the number of ORFs identified only in O. sativa genome, and the number in white box is the number of ORFs identified only in O. glaberrima genome.

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