Isolation of a Novel QTL, qSCM4, Associated with Strong Culm Affects Lodging Resistance and Panicle Branch Number in Rice

Abstract

Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an F₂ segregant population and a recombinant self-incompatible line population from the cross between Shennong265 (SN265) and Lijiangxintuanheigu (LTH) after multiple years and multiple environments. Then, the residual heterozygous derived segregant population which consisted of 1781 individual plants, and the BC₃F₂ segregant population which consisted of 3216 individual plants, were used to shorten the physical interval of qSCM4 to 58.5 kb including 11 genes. DNA sequencing revealed the most likely candidate gene for qSCM4 was Os04g0615000, which encoded a functional protein with structural domains of serine and cysteine. There were 13 DNA sequence changes in LTH compared to SN265 in this gene, including a fragment deletion, two base changes in the 3' UTR region, six base changes in the exons, and four base changes in the introns. A near-isogenic line carrying qSCM4 showed that it improved the lodging resistance through increasing stem thickness by 25.3% and increasing stem folding resistance by 20.3%. Furthermore, it was also discovered that qSCM4 enhanced the primary branch per panicle by 16.7%, secondary branch by per panicle 9.9%, and grain number per panicle by 14.7%. All the above results will give us a valuable genetic resource for concurrently boosting culm strength and lodging resistance, and they will also provide a basis for further research on the lodging resistance mechanism of rice.

Keywords: candidate gene; functional analysis; lodging resistance; qSCM4; rice.

Figure 1

Genomic locations of four QTLs with strong effects for lodging related traits identified in the RILs population. Green indicates positive effect inherited from LTH. Orange indicates positive effect inherited from SN265. 1–12 indicates chromosome 1 to chromosome 12.

Figure 2

Fine mapping and candidate gene analysis of the strong culm and lodging resistance QTL qSCM4: (a) genetic localization of qSCM4 in recombinant inbred lines population; (b) the genotypes of residual heterozygous line 08-3-2-1, The grey parts indicate the genotypes of the LTH, and the white indicate the genotypes of SH265; (c) fine mapping of qSCM4 in remaining heterozygous-derived populations; (d) fine mapping of qSCM4 in BC₃F₂ segregating populations, The grey parts indicate the genotypes of the LTH, and the white indicate the genotypes of SH265; (e) candidate gene prediction for qSCM4 region; and (f) candidate gene DNA sequence variation of qSCM4.

Figure 3

Analysis of yield and lodging-related traits in the near-isogenic lines with strong culm resistance QTL-qSCM4: (a) comparison of plant size of NILs; (b) cross section of the basal internode of NIL-qSCM4; (c) cross section of the basal internode stem of SN265; (d) the basal internode wall of NIL-qSCM4; (e) the basal internode stem wall of SN265; (f) comparison of plant height between two NILs; (g) comparison of breaking strength between two NILs; (h) comparison of grain number per panicle between two NILs; (i) comparison of the number of primary branch between two NILs; and (j) comparison of the number of secondary branch between two NILs. * p < 0.05, ** p < 0.01, using Student’s t-test.

Figure 4

The building process of F₂ population, RILs population, RHLs population and BC₃F₂ population used in this study.

Figure 5

The measurement for lodging resistance related traits in rice: (a) the measured instrument for breaking strength of the basal internode; (b) the internode of a rice plant; (c) the diameter and thickness of a cross-section of the middle point of the basal culm; and (d) the schematic of gravity center height.