Dissection of Pleiotropic QTL Regions Controlling Wheat Spike Characteristics Under Different Nitrogen Treatments Using Traditional and Conditional QTL Mapping

Abstract

Optimal spike characteristics are critical in improving the sink capacity and yield potential of wheat even in harsh environments. However, the genetic basis of their response to nitrogen deficiency is still unclear. In this study, quantitative trait loci (QTL) for six spike-related traits, including heading date (HD), spike length (SL), spikelet number (SN), spike compactness (SC), fertile spikelet number (FSN), and sterile spikelet number (SSN), were detected under two different nitrogen (N) supplies, based on a high-density genetic linkage map constructed by PCR markers, DArTs, and Affymetrix Wheat 660 K SNP chips. A total of 157 traditional QTLand 54 conditional loci were detected by inclusive composite interval mapping, among which three completely low N-stress induced QTL for SN and FSN (qSn-1A.1, qFsn-1B, and qFsn-7D) were found to maintain the desired spikelet fertility and kernel numbers even under N deficiency through pyramiding elite alleles. Twenty-eight stable QTL showing significant differencet in QTL detection model were found and seven genomic regions (R2D, R4A, R4B, R5A, R7A, R7B, and R7D) clustered by these stable QTL were highlighted. Among them, the effect of R4B on controlling spike characteristics might be contributed from Rht-B1. R7A harboring three major stable QTL (qSn-7A.2, qSc-7A, and qFsn-7A.3) might be one of the valuable candidate regions for further genetic improvement. In addition, the R7A was found to show syntenic with R7B, indicating the possibly exsting homoeologous candidate genes in both regions. The SNP markers involved with the above highlighted regions will eventually facilitate positional cloning or marker-assisted selection for the optimal spike characteristics under various N input conditions.

Keywords: conditional QTL mapping; low nitrogen tolerance; quantitative trait locus; spike characteristics; wheat.

Figure 1

Chromosomal locations of seven highlighted genomic regions for spike characteristics in this study. The red intervals on the chromosomes and regions represent the LOD-3 confidence interval of the location of each genomic region. To the left of the chromosomes: the centiMorgan (cm) interval is shown; the red rectangles represent each QTL region; the purple lines represent the putative location of the screened genes associated with spike-related traits; the black intervals represent the coincident QTL in previous reports (Reference 1 to Reference 11), and among them, three QTL in bold (qKnps-4A, qPh-4B, and qKn-4B) were detected using the same population of this study (KJ-RILs). On the right of each chromosomal region: the blue and green rectangles represent the QTL with positive alleles from KN9204 and J411, respectively; the letter C after parentheses represents the expression of QTL induced by N deficiency, and among them, C^* represents the QTL (qFsn-7D) is a completely LN-stress induced QTL. Reference 1: (Nishijima et al., 2017); Reference 2: (Cuthbert et al., 2008); Reference 3: (Cui et al., 2017); Reference 4: (Heidari et al., 2011); Reference 5: (Zhang et al., 2017); Reference 6: (Fan et al., 2015); Reference 7: (Zhai et al., 2016); Reference 8: (Xu et al., 2014).

Figure 2

The syntenic region between R7A and R7B. The number in parentheses following the SNP marker (e.g., AX-110483616) indicates the genetic position (cm); the number in the parentheses following predicted gene (e.g., TraesCS7A01G473100) indicates the physical position (Mb); the red shadow indicates the range of the syntenic region between R7A and R7B.