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Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

ABSTRACT: Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and 0-diversity genes during breeding. Using pedigree information, we also traced SNP transmission patterns and observed breeding signatures in pedigree. These regions included the larger number of key well-known functional genes. Besides, 35 regions spanning 0.16% of the rice gnome had been differentially selected between conventional and restorer pedigrees. These genes identified here will be useful to the further pedigree breeding. Our study provides insights into the genetic basis of backbone varieties and will have immediate implications for performing genome-wide breeding by design.

SUBMITTER: Zheng X

PROVIDER: S-EPMC5428501 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

Zheng Xingfei X Li Lanzhi L Liang Fan F Tan Changjun C Tang Shuzhu S Yu Sibin S Diao Ying Y Li Shuangcheng S Hu Zhongli Z

Scientific reports 20170322 1

Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and ...[more]

PMID: 28331200

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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.

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.

Dataset Information

Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

Publications

Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

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