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 histor...

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Autores principales:	Xingfei Zheng, Lanzhi Li, Fan Liang, Changjun Tan, Shuzhu Tang, Sibin Yu, Ying Diao, Shuangcheng Li, Zhongli Hu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f7a8031220194235b2260352c48c4471
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spelling	oai:doaj.org-article:f7a8031220194235b2260352c48c44712021-12-02T12:32:19ZPedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement10.1038/s41598-017-00415-12045-2322https://doaj.org/article/f7a8031220194235b2260352c48c44712017-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00415-1https://doaj.org/toc/2045-2322Abstract 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.Xingfei ZhengLanzhi LiFan LiangChangjun TanShuzhu TangSibin YuYing DiaoShuangcheng LiZhongli HuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xingfei Zheng Lanzhi Li Fan Liang Changjun Tan Shuzhu Tang Sibin Yu Ying Diao Shuangcheng Li Zhongli Hu Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
description	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.
format	article
author	Xingfei Zheng Lanzhi Li Fan Liang Changjun Tan Shuzhu Tang Sibin Yu Ying Diao Shuangcheng Li Zhongli Hu
author_facet	Xingfei Zheng Lanzhi Li Fan Liang Changjun Tan Shuzhu Tang Sibin Yu Ying Diao Shuangcheng Li Zhongli Hu
author_sort	Xingfei Zheng
title	Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
title_short	Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
title_full	Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
title_fullStr	Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
title_full_unstemmed	Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
title_sort	pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f7a8031220194235b2260352c48c4471
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Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement

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