Comprehensive QTL analyses of nitrogen use efficiency in indica rice

Abstract

Nitrogen-use efficiency (NUE) in rice is a complex quantitative trait involved in multiple biological processes and agronomic traits; however, the genetic basis and regulatory network of NUE remain largely unknown. We constructed a high-resolution microarray-based genetic map for 261 recombinant inbred lines derived from two indica parents. Using 2,345 bin markers, comprehensive analyses of quantitative trait loci (QTLs) of seven key agronomic traits under two different N levels were performed. A total of 11 non-redundant QTLs for effective panicle number (EPN), 7 for grain number per panicle, 13 for thousand-grain weight, 2 for seed-setting percentage, 15 for plant height, 12 for panicle length, and 6 for grain yield per plant were identified. The QTL regions were as small as 512 kb on average, and more than half spanned an interval smaller than 100 kb. Using this advantage, we identified possible candidate genes of two major EPN-related QTLs. One QTL detected under both N levels possibly encodes a DELLA protein SLR1, which is known to regulate NUE, although the natural variations of this protein have not been reported. The other QTL detected only under a high N level could encode the transcription factor OsbZIP59. We also predicted the possible candidate genes for another three of the NUE-related QTLs. Our results provide a reference for improving NUE-related QTL cloning and promote our understanding of NUE regulation in indica rice.

Identification and characterization of stripe rust, leaf rust, leaf spot, and common bunt resistance in spring wheat

“…However, there have been numerous cases of disagreement between the genetic and physical maps in terms of positional and chromosomal assignment (DeWan et al., 2002). As a result, the chromosome locations and positions of several QTLs have been found erroneous (Semagn et al., 2021) and several putative QTLs were likely redundant (Liu et al., 2022; Yonemaru et al., 2010; Zhao et al., 2018). The use of IWGSC RefSeq plays an important role in improving genetic maps using fixed locus order and/or the use of the physical positions directly in QTL mapping or presenting QTL results as has been the case in the current study.…”