Identification of Rice QTLs for Important Agronomic Traits with Long-Kernel CSSL-Z741 and Three SSSLs

doi:10.1016/j.rsci.2020.04.008

Abstract

Abstract:

Rice kernel shape affects kernel quality (appearance) and yield (1000-kernel weight) and therefore is an important agronomic trait, but its inheritance is complicated. We identified a long-kernel rice chromosome segment substitution line (CSSL), Z741, derived from Nipponbare as a recipient and Xihui 18 as a donor parent. Z741 has six substitution segments distributed on rice chromosomes 3, 6, 7, 8 and 12 with an average replacement length of 5.82 Mb. Analysis of a secondary F₂ population from a cross between Nipponbare and Z741 identified 20 QTLs for important agronomic traits. The kernel length of Z741 is controlled by a major QTL (qKL3) and a minor QTL (qKL7). Candidate gene prediction and sequencing indicated that qKL3 may be an allele of OsPPKL1, which encodes a protein phosphatase implicated in brassinosteroid signaling, and qKL7 is an unreported QTL. Finally, we validated eight QTLs (qKL3, qKL7, qRLW3-1, qRLW7, qPH3-1, qKWT3, qKWT7 and qNPB6) using three selected single- segment substitution lines (SSSLs), S1, S2 and S3. Also, we detected five QTLs (qKL6, qKW3, qKW7, qKW6 and qRLW6) in S1, S2 and S3, which were not found in the Nipponbare/Z741 F₂ population. However, qNPB3, qNPB7 and qPL3 QTLs were not validated by the three SSSLs in 2019, suggesting that minor QTLs are susceptible to environmental factors. These results lay the foundation for studying the biodiversity of kernal length and molecular breeding of different kernel types.

Key words: chromosome segment substitution line, single-segment substitution line, kernel shape, quantitative trait locus, rice

Hui Wang, Jiayu Zhang, Farkhanda Naz, Juan Li, Shuangfei Sun, Guanghua He, Ting Zhang, Yinghua Ling, Fangming Zhao. Identification of Rice QTLs for Important Agronomic Traits with Long-Kernel CSSL-Z741 and Three SSSLs[J]. Rice Science, 2020, 27(5): 414-422.

Figures/Tables 7

Fig. 1. Chromosome substitution segments of Z741 and QTLs identified in them.Physical distances (Mb) and mapped QTLs are marked to the left of each chromosome. Markers and lengths of the substitution segments are displayed to the right. Black sections on each chromosome indicate the substitution segments.KL, Kernel length; KPP, Number of kernel per panicle; KWT, 1000-kernel weight; NPB, Number of primary branches per plant; NSB, Number of secondary branches per plant; PH, Plant height; PL, Panicle length; PN, Number of panicles per plant; RLW, Ratio of length to width; SPP, Number of spikelets per panicle, SSR, Seed-setting rate.

Supplemental Table 1 Agronomic traits of Z741 and Nipponbare and statistical parameters of F2 population.

Supplemental Fig. 1. Phenotypes of Nipponbare and Z741.A, Whole-plant phenotype of Nipponbare and Z741 at the milky stage. B, Kernel shape of Nipponbare and Z741.

Table 2 QTLs for agronomic traits.

Table 3 Additive effect analysis of QTLs in three single-segment substitution lines S1, S2 and S3.

Fig. 2. Kernel lengths of Nipponbare and three single-segment substitution lines S1, S2 and S3.Left, Images of aligned kernels for lines of given genotypes; Right, Statistics of kernel length. μ, Mean value of kernel lengths; A, Additive effect value for each QTL controlling kernel length.

Fig. 3. Comparison of OsPPKL1 sequences in Nipponbare and Z741.A, Sketch map of OsPPKL1 (Os03g0646900) gene. Green boxes refer to exons, white boxes refer to introns and 3′-UTR. Red arrows indicate the alteration of a codon. B, Different sequences of OsPPKL1 between Nipponbare and Z741. Yellow indicates conserved sequence, and black arrows mark mutation sites.

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