Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.)

Abstract

Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized. QPht/Sl.cau-2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau-2D.2 is mapped between two SSR markers, SSR-2062 and Xgwm484, which are located on the same genomic interval as Rht8. Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau-2D.1 is much lower than that of QPht/Sl.cau-2D.2, suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8, a significant difference in cell length was observed between the NILs of QPht/Sl.cau-2D.2. By contrast, there was no difference in cell length between NILs of QPht/Sl.cau-2D.1, indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau-2D.1 and/or QPht/Sl.cau-2D.2 with the other genes in wheat breeding.

Fig. 1

Saturated genetic linkage map of chromosome 2D in the RIL population and the collinearity of the developed markers, Aegilops tauschii markers and corresponding physical position in the Chinese Spring RefSeq v1.0 sequence. The red segment means the heterozygous segment in RIL171 (color figure online)

Fig. 2

Dissection of QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2. a QTL mapping using a saturate genetic map. b Graphical genotypes of two populations (derived from RIL 171). c Performance of the members of two NIL pairs in three field trails. *** indicate significant differences at the 0.001 levels (Student’s t test)

Fig. 3

Culm and spike morphology of the NILs of QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2 grown in Beijing (2016–2017 growing season). a Main tillers. Bars = 10 cm. b Spikes, peduncles and other internodes of NIL-I^Y8679 (left) and NIL-I^J411 (right). The bar represents 5 cm. c Spikes, peduncles and the internodes of NIL-II^Y8679 (left) and NIL-II^J411 (right). The bar represents 5 cm. PED, peduncle; 1I, first internode under peduncle; 2I, the second internode under peduncle; 3I, the third internode under peduncle; and 4I, the fourth internode under peduncle

Fig. 4

Difference in PHT and SL between two alleles of STARP-2001 and SSR-2433 in the RIL population of five environments and one combined analysis (BLUP). The values represent the means (± SD) of RILs with the same genotype. *, **, *** indicate significant differences at the 0.05, 0.01, 0.001 levels (Student’s t test), respectively. STARP-2001-Y, the group with Y8679 type; STARP-2001-J, the group with J411 type; SSR-2433-Y, the group with Y8679 type; SSR-2433-J, the group with J411 type. The x-axis, five environments and one combined analysis(BLUP): E1, Beijing, 2010–2011; E3, Beijing, 2011–2012; E5, Anhui, 2012–2013; E7, Shaanxi, 2012–2013; E8, Beijing, 2014–2015; C indicates the combined QTL analysis based on the BLUP values across nine environments. a PHT between two alleles of STARP-2001. b SL between two alleles of STARP-2001. c PHT between two alleles of SSR-2433. d SL between two alleles of SSR-2433

Fig. 5

Haplotype distributions of STARP-2001 and SSR-2433 in 724 common wheat varieties/lines from China (a, b) and 442 common wheat varieties/lines from other countries (c, d). I, Northern winter wheat region; II, Yellow and Huai River valley winter wheat region; III, low and middle Yangtze River valley winter wheat region; IV, south-western winter wheat region; V, southern winter wheat region; VI, north-eastern spring wheat region; VII, northern spring wheat region; VIII, north-western spring wheat region; IX, Qinghai–Tibet spring–winter wheat region; X, Xinjiang winter–spring wheat region

Fig. 6

Longitudinal culm sections of NILs of QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2 from the flowering stage. Scanning micrographs of the medial zone of the fully elongated peduncle in a NIL-I^Y8679, b NIL-I^J411, c NIL-II^Y8679 and d NIL-II^J411. Bars = 100 μm. Comparisons of parenchymatic cell length (μm) in medial sections of the peduncle from e NILs of QPht/Sl.cau-2D.1 and fQPht/Sl.cau-2D.2. NS, no significance P = 0.05; ***, t test P < 0.001. Bars represent the standard deviation

Fig. 7

PCR products of STARP-2001 (a) and SSR-2433 (b) in several hexaploid wheat accessions and Aegilops tauschii accessions

Fig. 8

Structure of candidate genes showing the nucleotide and amino acid sequences polymorphism between Y8679 and J411. Lines, blue boxes and white boxes represent introns, exons and untranslated regions in the gene, respectively. Nucleotide and amino acid sequences of Y8679 and J411 are shown in red and black font, respectively. The numbers in bracket represent the positions of nucleotide or amino acid sequences relative to ATG. – represents deletion. F.S. indicates frame shift. a Structure of TraesCS2D01G051500. b Structure of TraesCS2D01G055700. c Structure of TraesCS2D01G058700 (color figure online)