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Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

ABSTRACT: Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

SUBMITTER: Zhang J

PROVIDER: S-EPMC5024649 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

Zhang Jianwei J Chen Ling-Ling LL Xing Feng F Kudrna David A DA Yao Wen W Copetti Dario D Mu Ting T Li Weiming W Song Jia-Ming JM Xie Weibo W Lee Seunghee S Talag Jayson J Shao Lin L An Yue Y Zhang Chun-Liu CL Ouyang Yidan Y Sun Shuai S Jiao Wen-Biao WB Lv Fang F Du Bogu B Luo Meizhong M Maldonado Carlos Ernesto CE Goicoechea Jose Luis JL Xiong Lizhong L Wu Changyin C Xing Yongzhong Y Zhou Dao-Xiu DX Yu Sibin S Zhao Yu Y Wang Gongwei G Yu Yeisoo Y Luo Yijie Y Zhou Zhi-Wei ZW Hurtado Beatriz Elena Padilla BE Danowitz Ann A Wing Rod A RA Zhang Qifa Q

Proceedings of the National Academy of Sciences of the United States of America 20160817 35

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parent ...[more]

PMID: 27535938

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Project description:Background and aimsUnderstanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined.MethodsSeeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis.Key resultsThe seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], -σ-1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22-1.86.ConclusionsThis is the first study to describe the extent of variation in σ within a species' variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.

Project description:BackgroundThe increasing temperatures due to climate change around the world poses a serious threat to sustainable crop production. The growing adverse effects of heat stress are putting global food security at great risk. Crop improvement for adaptation to increased temperatures is therefore of paramount importance. This study aims at assessing the effects of heat stress in relation to agro-morphological and physiological traits of six rice varieties. The study was carried out in the Township of Glazoué, a rice-growing area in Benin. The experiments were laid in randomized complete block design with three replications. Two types of stress were imposed: high-temperature stress in the dry season and optimal temperatures in the rainy season. The calculated mean values of morphological, physiological, and agronomic traits were used to estimate heritability, genetic advance, PCA, and correlation.ResultsThe results showed that heat stress had a significant (p ≤ 0.01) influence on plant height, leaf length, number of tillers, number of internodes, days to flowering, and days to maturity, 1000-seed weight, and yield per plant. The heat stress had significantly delayed the flowering of all the varieties when compared to the controls. The highest values of 1000-seed weight (34. 67 g) were recorded for BRIZ-8B while the lowest (25.33 g) were recorded for NERICA-L20. The highest values for the genotypic coefficient of variation (43.05%) and phenotypic coefficient of variation (99.13%) were recorded for yield per plant under heat stress. The topmost broad-sense heritability was recorded for grain width (92.72%), followed by days to maturity (69.33%), days to flowering (68.50%), number of grains per panicle (57.35%), and yield (54.55%).ConclusionsThese results showed that BRIZ-8B and BRIZ-10B were the most tolerant to high temperature amongst the six varieties assessed and potentially could be recommended to farmers for production under high temperature and be used in breeding programs to improve heat tolerance in rice.

Dataset Information

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

Publications

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

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