QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice.

Congcong Shen,Jauhar Ali,Jiantao Chen,Shuangbin Zhu,Yanru Cui,Jianlong Xu,Kai Chen,Yajun Zhu,Xuefei Mi,Zhikang Li,Guoyou Ye

doi:10.3389/fgene.2021.616428

Abstract

Nitrogen is one of the most important nutrients for rice growth and development. Breeding of nitrogen deficiency tolerance (NDT) variety is considered to be the most economic measure to solve the constrain of low nitrogen stress on grain yield in rice. An interconnected breeding (IB) population of 497 lines developed using Huanghuazhan (HHZ) as the recurrent parent and eight elite lines as the donor parents were tested for five traits including grain yield, biomass, harvest index, thousand grain weight, and spikelet fertility under two nitrogen treatments in three growing seasons. Association analysis using 7,388 bins generated by sequencing identified a total of 14, 14, and 12 QTLs for the five traits under low nitrogen (LN), normal nitrogen (NN), and LN/NN conditions, respectively, across three seasons. Favorable alleles were dissected for the 40 QTLs at the 10 NDT regions, and OM1723 was considered as the most important parent with the highest frequency of favorable alleles contributing to NDT-related traits. Six superior lines all showed significantly higher GY in LN environments and similar GY under NN environments except for H10. Substitution mapping using near-isogenic introgression lines delimited the qTGW2-1, which was identified on chromosome 2 under LN, NN, and LN/NN conditions into two QTLs, which were located in the two regions of about 200 and 350 kb with different favorable alleles. The bins 16, 1301, 1465, 1486, 3464, and 6249 harbored the QTLs for NDT detected in this study, and the QTLs/genes previously identified for NDT or nitrogen use efficiency (NUE) could be used for enhancing NDT and NUE by marker-assisted selection (MAS).

Highlights

Rice (Oryza sativa L.) is one of the most important staple crops in the world and the main calorie source for more than 65% of the population in China
Grain yield and biomass per plant (BM) were much higher in the NN than in the low nitrogen (LN), while Harvest index (HI) and spikelet fertility (SF) were similar in the two nitrogen treatments (Table 1)
Many agronomic traits such as effective tiller number, biomass, and grain yield have been studied under low-N stress in rice, and some QTLs associated with N translocation were found to locate in the same chromosomal regions (Shan et al, 2005; Tong et al, 2006; Senapathy et al, 2008)

Summary

Introduction

Rice (Oryza sativa L.) is one of the most important staple crops in the world and the main calorie source for more than 65% of the population in China. Many QTLs/genes for NDT, measured as the relative trait values under low nitrogen (LN) stress to normal nitrogen (NN) conditions have been reported by QTL mapping and gene expression methods. QTLs were detected for the traits or the relative trait values of seedling height, shoot dry weight, chlorophyll content (Tong et al, 2011), maximum root length, root dry weight, plant dry weight (Lv et al, 2010; Zhao et al, 2014) at seedling stage, spikelet fertility percentage (Shan et al, 2005), grain yield (Tong et al, 2006), panicle number and total panicle weight (Wang et al, 2009), grain number per panicle, spikelet fertility percentage and 100-grain weight (Tong et al, 2011), and nitrogen efficiency (Tang et al, 2011) at maturity stage using populations such as backcross, chromosome segment substitution line, and recombinant inbred lines under LN stress or different nitrogen level conditions. Fifteen QTLs were identified for the four NDT traits including relative grain yield, relative biomass, relative grain nitrogen, and relative biomass nitrogen (Wei et al, 2012), and some of which are close to genes controlling nitrogen cycle

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Conclusion