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. 2021 Nov 19:12:775051.
doi: 10.3389/fpls.2021.775051. eCollection 2021.

High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Fei Li  1 , Zhenyun Han  1 , Weihua Qiao  1 , Junrui Wang  1   2 , Yue Song  1 , Yongxia Cui  1   3 , Jiaqi Li  1   4 , Jinyue Ge  1 , Danjing Lou  1 , Weiya Fan  1 , Danting Li  5 , Baoxuan Nong  5 , Zongqiong Zhang  5 , Yunlian Cheng  1 , Lifang Zhang  1 , Xiaoming Zheng  1 , Qingwen Yang  1
Affiliations

High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Fei Li et al. Front Plant Sci. .

Abstract

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.

Keywords: QTL mapping; comparative genomics; genetic map; reference genome; weedy rice.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Agronomic characteristics of LM8 and Shen 08S (parents) and the genetic map constructed based on the F2 population. (A) Plant height of LM8 (right) and Shen 08S (left). Bar = 10 cm. (B) Panicle length of LM8 (right) and Shen 08S (left). Bar = 0.5 cm. (C) Branches of LM8 (right) and Shen 08S (left). Bar = 2 cm. (D) Grain size of LM8 (bottom) and Shen 08S (above). Bar = 1 cm. (E) Genomic locations of 12 agronomic trait associated QTLs are illustrated on the 12 linkage groups. PH, plant height; TN, tillering number; FLL, flag leaf length; FLW, flag leaf width; PL, panicle length; PB, primary branch number; SB, secondary branch number; GL, grain length; GW, grain width; GT, grain thickness; LWR, length to width ratio; TGW, thousand-grain weight.
FIGURE 2
FIGURE 2
Frequency distribution of the 12 agronomic traits in the F2 population. (A) GL, grain length. (B) GW, grain width. (C) GT, grain thickness. (D) LWR, length to width ratio. (E) TGW, thousand-grain weight. (F) PL, panicle length. (G) PH, plant height. (H) PB, primary branch number. (I) SB, secondary branch number. (J) TN, tillering number. (K) FLL, flag leaf length. (L) FLW, flag leaf width.
FIGURE 3
FIGURE 3
QTL for grain length and prediction of candidate genes. (A) QTL mapping results for grain length and seven putative genes (ORUFILM03g000096, ORUFILM03g000095, ORUFILM03g000094, ORUFILM03g000093, ORUFILM03g000092, ORUFILM03g000091, and ORUFILM03g000090) within the region. (B) Gene structure of ORUFILM03g000095 (top), (C) grain length (GL) distribution in each genotype of ORUFILM03g000095, (D) corresponding GL phenotypes in F2 individuals (lower right). Asterisks is correlation between genotype and phenotype, *P < 0.05. **P < 0.01.
FIGURE 4
FIGURE 4
The morphology and genome features of LM8. (A) Whole plants, bar = 10 cm. (B) Panicles, bar = 2 cm. (C) Grains, bar = 1 cm. (D) Genome features of LM8. Circles from inside to outside are transposable element (TE) content, repeat density, gene density, and GC density.
FIGURE 5
FIGURE 5
Comparative genomics analyses of LM8 with other Oryza genomes. (A) Statistics of gene families in 18 Oryza genomes. (B) Core and dispensable genes from five reference genomes. The numbers in the species section and overlapping section indicate the numbers of specific and shared gene families, respectively. IND, O. sativa ssp. indica. JAP, O. sativa ssp. japonica. RUF, O. rufipogon. NIV, O. nivara. and LM8, O. sativa f. spontanea. (C) Phylogenetic relationships and grain phenotypes of LM8 and other Oryza genomes. Pie charts represent total gene families, consisting of contracted gene families (red), expanded gene families (green), and unchanged gene families (blue). The numbers of genes in expanded (+) and contracted (–) gene families in each rice variety are shown with the rice variety name farthest to the right. The lineage divergence times are indicated on the nodes and nodes marked in red are known fossil time points. O. brachyantha was used as the outgroup. MRCA, most recent common ancestor. AUS, O. aus. IND, O. sativa ssp. indica. JAP, O. sativa ssp. japonica. GLA, O. glaberrima. BAR, O. barthii. GLU, O. glumaepatula. MER, O. meridionalis. RUF, O. rufipogon. NIV, O. nivara. LON, O. longistaminata. PUN, O. punctata. BRA, O. brachyantha. JX-6, O. rufipogon var. JX-6. Z59, O. rufipogon var. Z59. MH63, O. sativa ssp. indica var. Minghui63. ZS97, O. sativa ssp. indica var. Zhenshan97. R498, O. sativa ssp. indica var. Shuihui498. and LM8, O. sativa f. spontanea.
FIGURE 6
FIGURE 6
Collinearity between LM8 and two cultivated rice (JAP and R498) genomes. (A) Collinearity between JAP and LM8. (B) Collinearity between R498 and LM8.
FIGURE 7
FIGURE 7
Venn diagrams showing specific and shared gene families between LM8 and other Oryza genomes in the same cluster of the evolution tree. (A) JAP, RUF, JX6, Z59 and LM8. (B) LON, MER, PUN, BRA and LM8. (C) MH63, R498, ZS97 and LM8. (D) AUS, NIV, IND and LM8. (E) BAR, GLU, GLA, and LM8. AUS, O. aus. IND, O. sativa ssp. indica. JAP, O. sativa ssp. japonica. GLA, O. glaberrima. BAR, O. barthii. GLU, O. glumaepatula. MER, O. meridionalis. RUF, O. rufipogon. NIV, O. nivara. LON, O. longistaminata. PUN, O. punctata. BRA, O. brachyantha. JX-6, O. rufipogon var. JX-6. Z59, O. rufipogon var. Z59. MH63, O. sativa ssp. indica var. Minghui63. ZS97, O. sativa ssp. indica var. Zhenshan97. R498, O. sativa ssp. indica var. Shuihui498. and LM8, O. sativa f. spontanea.
FIGURE 8
FIGURE 8
Statistics of the GO enrichment analysis of the expanded gene families. The x-axis represents the percentage of enriched genes to the total annotated genes. The y-axis indicates the entry of each enrichment category. The size of the dots corresponds to the number of enriched genes, and the color panel on the right indicates the q-value. The lower the value, the more significant it is.
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