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具有和不具有稻属红稻渗入的水稻杂种的全基因组转录组图谱揭示了产量的候选基因。

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield.

机构信息

ICAR-Indian Institute of Rice Research, Hyderabad, 500 030, India.

CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500 007, India.

出版信息

Sci Rep. 2020 Mar 17;10(1):4873. doi: 10.1038/s41598-020-60922-6.

DOI:10.1038/s41598-020-60922-6
PMID:32184449
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7078188/
Abstract

In this study, we compared genome-wide transcriptome profile of two rice hybrids, one with (test hybrid IR79156A/IL50-13) and the other without (control hybrid IR79156A/KMR3) O. rufipogon introgressions to identify candidate genes related to grain yield in the test hybrid. IL50-13 (Chinsurah Nona2 IET21943) the male parent (restorer) used in the test hybrid, is an elite BCF introgression line of KMR3 with O. rufipogon introgressions. We identified 2798 differentially expressed genes (DEGs) in flag leaf and 3706 DEGs in panicle. Overall, 78 DEGs were within the major yield QTL qyld2.1 and 25 within minor QTL qyld8.2. The DEGs were significantly (p < 0.05) enriched in starch synthesis, phenyl propanoid pathway, ubiquitin degradation and phytohormone related pathways in test hybrid compared to control hybrid. Sequence analysis of 136 DEGs from KMR3 and IL50-13 revealed 19 DEGs with SNP/InDel variations. Of the 19 DEGs only 6 showed both SNP and InDel variations in exon regions. Of these, two DEGs within qyld2.1, Phenylalanine ammonia- lyase (PAL) (Os02t0626400-01, OsPAL2) showed 184 SNPs and 11 InDel variations and Similar to phenylalanine ammonia- lyase (Os02t0627100-01, OsPAL4) showed 205 SNPs and 13 InDel variations. Both PAL genes within qyld2.1 and derived from O. rufipogon are high priority candidate genes for increasing grain yield in rice.

摘要

在这项研究中，我们比较了两个水稻杂种的全基因组转录组谱，一个具有（测试杂种 IR79156A/IL50-13）和另一个没有（对照杂种 IR79156A/KMR3）O. rufipogon 导入，以鉴定与测试杂种中粒产量相关的候选基因。IL50-13（Chinsurah Nona2 IET21943）是测试杂种中的雄性亲本（恢复系），是具有 O. rufipogon 导入的 KMR3 的优秀 BCF 导入系。我们在旗叶中鉴定出 2798 个差异表达基因（DEGs），在穗中鉴定出 3706 个 DEGs。总体而言，78 个 DEGs 位于主要产量 QTL qyld2.1 内，25 个位于次要 QTL qyld8.2 内。与对照杂种相比，测试杂种中这些 DEGs 在淀粉合成、苯丙烷途径、泛素降解和植物激素相关途径中显著（p < 0.05）富集。从 KMR3 和 IL50-13 中分析的 136 个 DEGs 的序列显示，有 19 个 DEGs 具有 SNP/InDel 变异。在这 19 个 DEGs 中，只有 6 个在exon 区域显示 SNP 和 InDel 变异。在这些基因中，位于 qyld2.1 内的两个 DEGs，苯丙氨酸解氨酶（PAL）（Os02t0626400-01，OsPAL2）显示 184 个 SNP 和 11 个 InDel 变异，而类似于苯丙氨酸解氨酶（Os02t0627100-01，OsPAL4）显示 205 个 SNP 和 13 个 InDel 变异。位于 qyld2.1 内的这两个 PAL 基因都来自 O. rufipogon，是提高水稻粒产量的高优先级候选基因。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/c1813791efee/41598_2020_60922_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/245e15212422/41598_2020_60922_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/00fc4f62fed4/41598_2020_60922_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/514ca1b12522/41598_2020_60922_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/c1813791efee/41598_2020_60922_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/245e15212422/41598_2020_60922_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/00fc4f62fed4/41598_2020_60922_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/514ca1b12522/41598_2020_60922_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf9f/7078188/c1813791efee/41598_2020_60922_Fig4_HTML.jpg

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