Sevanthi Amitha Mithra, Sinha Subodh Kumar, V Sureshkumar, Rani Manju, Saini Manish Ranjan, Kumari Sapna, Kaushik Megha, Prakash Chandra, K Venkatesh, Singh G P, Mohapatra Trilochan, Mandal Pranab Kumar
ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India.
Rice (N Y). 2021 Jun 5;14(1):49. doi: 10.1186/s12284-021-00487-8.
We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root parameters, except for root length under N-W+, N22 performed better than IR64. Chlorophyll a, b and carotenoid content were higher in IR64 under N+W+ treatment and N-W+ and N+W- stresses; however, under dual stress, N22 had higher chlorophyll b content. While nitrite reductase, glutamate synthase (GS) and citrate synthase assays showed better specific activity in IR64, glutamate dehydrogenase showed better specific activity in N22 under dual stress (N-W-); the other N and C assimilating enzymes showed similar but low specific activities in both the genotypes. A total of 8926 differentially expressed genes (DEGs) were identified compared to optimal (N+W+) condition from across all treatments. While 1174, 698 and 903 DEGs in IR64 roots and 1197, 187 and 781 in N22 roots were identified, nearly double the number of DEGs were found in the shoot tissues; 3357, 1006 and 4005 in IR64 and 4004, 990 and 2143 in N22, under N-W+, N+W- and N-W- treatments, respectively. IR64 and N22 showed differential expression in 15 and 11 N-transporter genes respectively, under one or more stress treatments, out of which four showed differential expression also in N+W- condition. The negative regulators of N- stress, e.g., NIGT1, OsACTPK1 and OsBT were downregulated in IR64 while in N22, OsBT was not downregulated. Overall, N22 performed better under dual stress conditions owing to its better root architecture, chlorophyll and porphyrin synthesis and oxidative stress management. We identified 12 QTLs for seed and straw N content using 253 recombinant inbred lines derived from IR64 and N22 and a 5K SNP array. The QTL hotspot region on chromosome 6 comprised of 61 genes, of which, five were DEGs encoding for UDP-glucuronosyltransferase, serine threonine kinase, anthocyanidin 3-O-glucosyltransferase, and nitrate induced proteins. The DEGs, QTLs and candidate genes reported in this study can serve as a major resource for both rice improvement and functional biology.
我们在此报告了两种水稻基因型，即IR 64（IR64）和Nagina 22（N22）的根和地上部组织在低氮（N-W+）、低水（N+W-）和双重胁迫（N-W-）条件下全基因组的变化，以及它们与氮利用效率QTL的关联。对于所有根系参数，除了N-W+条件下的根长外，N22的表现均优于IR64。在N+W+处理以及N-W+和N+W-胁迫下，IR64中的叶绿素a、b和类胡萝卜素含量较高；然而，在双重胁迫下，N22的叶绿素b含量较高。虽然亚硝酸还原酶、谷氨酸合酶（GS）和柠檬酸合酶的活性在IR64中表现更好，但在双重胁迫（N-W-）下，谷氨酸脱氢酶在N22中的活性表现更好；其他氮和碳同化酶在两种基因型中的活性表现相似但较低。与最佳（N+W+）条件相比，在所有处理中总共鉴定出8926个差异表达基因（DEG）。在IR64根中鉴定出1174、698和903个DEG，在N22根中鉴定出1197、187和781个DEG，而在地上部组织中发现的DEG数量几乎是根中的两倍；在N-W+、N+W-和N-W-处理下，IR64中分别为3357、1006和4005个，N22中分别为4004、990和2143个。在一种或多种胁迫处理下，IR64和N22分别在15个和11个氮转运蛋白基因中表现出差异表达，其中四个在N+W-条件下也表现出差异表达。氮胁迫的负调控因子，如NIGT1、OsACTPK1和OsBT在IR64中被下调，而在N22中，OsBT未被下调。总体而言，N22在双重胁迫条件下表现更好，这归因于其更好的根系结构、叶绿素和卟啉合成以及氧化应激管理。我们使用源自IR64和N22的253个重组自交系和一个5K SNP阵列鉴定了12个种子和秸秆氮含量的QTL。第6号染色体上的QTL热点区域由61个基因组成，其中五个是DEG，编码UDP-葡糖醛酸基转移酶、丝氨酸苏氨酸激酶、花青素3-O-葡糖基转移酶和硝酸盐诱导蛋白。本研究中报道的DEG、QTL和候选基因可作为水稻改良和功能生物学的重要资源。
