QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F2 Population

doi:10.1016/j.rsci.2018.04.001

摘要/Abstract

. [J]. Rice Science, 2018, 25(3): 121-131.

图/表 9

Fig. 1. Morphological characteristics of the parents and F1 generations.Left, Female parent; Middle, Male parent; Right, F1. Bars in A and B are 20 cm whereas bars in C and D are 5 mm.

Fig. 2. Frequency distribution of grain trait performance in the NIL-F2 population and construction of two extremely bulks based on the segregation of grain length.

Table 1 Summary of the paired-end sequencing results.

Sample ^a	No. of raw reads	No. of clean reads	Raw base (Gb)	Clean base (Gb)	Percentage of high quality base ^b (%)	GC content (%)	Average depth	Genome coverage (%)
H12-29	127 306 420	123 917 740	15.91	15.23	98.33	43.47	40.02×	92.13
FH212	115 010 274	112 007 606	14.38	13.77	98.35	43.56	36.12×	91.89
L-bulk	121 555 464	117 864 724	15.19	14.48	98.30	43.77	37.85×	92.57
S-bulk	128 780 448	125 643 324	16.10	15.46	98.42	43.85	40.43×	92.50

Table 2 Number of single nucleotide polymorphisms (SNPs) and InDels detected in pools and parental lines.

Sample	No. of SNPs	No. of InDels
H12-29	3 525 128	421 211
FH212	3 539 142	415 224
L-bulk	3 620 518	425 506
S-bulk	3 627 828	428 012

Fig. 3. Distribution of 455 262 SNPs used in QTL-seq analysis on rice genome. Chr, Chromosome; SNP, Single nucleotide polymorphism. X-axis is the position of SNP on chromosome. Different colors represent the density of SNPs within a sliding window of 50 kb.

Fig. 4. Δ(SNP-index) graph for the whole genome was plotted by plotting the average Δ(SNP-index) using a sliding window of 1 Mb with a step of 10 kb. SNP, Single nucleotide polymorphism. Each spot represents a SNP, and X-axis corresponds to the position of rice genome. Red line is the average value of Δ(SNP-index). Δ(SNP-index) plot with the statistical confidence interval under the null hypothesis of no QTL (P < 0.05, blue line; P < 0.01, purple line). A significant region on chromosome 5 (black box) was identified for grain length and weight (15-20 Mb).

Fig. 5. Mapping of qTGW5.3. A to C, SNP-index graphs of L-bulk and S-bulk, and Δ(SNP-index) from QTL-seq analysis, respectively; D, Graphical genomic regions of the eight recombinants and the location of qTGW5.3 identified for grain length and weight. Chr, Chromosome.

Table 3 Sequences and physical location of the markers.

Marker	Physical position (bp) ^a		Forward primer	Reverse primer
HX5009	15 151 174-	15 151 528	AAACAAGAGCCAAAGAAGTCA	TTCCGCTACATCCAACAAATA
HX5022	15 580 256-	15 580 414	AACGCTCACCTACAGATT	GTAATGAACAGGCGAATT
HX5018	15 722 159-	15 722 347	TCAGCATCGGAACAAATC	GAAGGGACGGACAGAAAC
HX5003	16 285 064-	16 285 514	CTCAGGAAGGTAGTCCGAGTCAT	CACAAGCCGTCAAGTTTATCACA
HX5005	17 602 063-	17 602 197	GGCAATACCAATCTATCGCCTCT	GCTGGCACCATTATCAAAGTTCA
HX5008	19 224 457-	19 224 922	CGTTCAGGCTTGTCTTCTTCTTAC	AATCACGGCTCCACCTGTTATTT

Table 4 QTL analysis in near isogenic line (NIL) populations.

Trait	Homozygous genotypic groups (Mean ± SD)		P	A	R² (%)
Trait	NIL^H12-29	NIL^FH212	P	A	R² (%)
GL (mm)	8.98 ± 0.07	6.70 ± 0.07	< 0.0001	-1.14	99.64
GW (mm)	2.57 ± 0.02	2.79 ± 0.02	< 0.0001	0.11	95.51
TGW (g)	24.53 ± 0.49	18.30 ± 0.55	< 0.0001	-3.11	97.32
NPP	6.40 ± 0.90	6.00 ± 0.80	0.0457	-0.24	6.34
NGP	171.80 ± 16.90	182.10 ± 20.0	0.0191	5.12	7.27
NSP	191.90 ± 20.10	203.30 ± 16.90	0.006	5.72	8.85
GY (g)	27.13 ± 4.85	19.95 ± 3.89	< 0.0001	-3.59	40.65

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