Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice

Abstract

Background Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where the japonica rice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production. Results Here, we re-sequence 200 japonica rice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungus Magnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance. Conclusions This is the first large-scale genomic landscape analysis of japonica rice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.

Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars

“…As reported in previous studies, NAL1 improved yield and altered the plant type by increasing the leaf blade width, number of secondary branches per panicle, GN, and grain yield per plant ( Zhang et al., 2014 ), and DTH7 greatly delayed rice heading and enhanced grain productivity ( Gao et al., 2014 ). Notably, both of these two genes were also identified in selective sweeps for improvement in GJ rice of central China ( Xiao et al., 2021 ). Interestingly, the domestication gene PROG1 was identified in our selective sweeps.…”

“…Because of the possibility of population structure, bottleneck, random drift, etc., we considered 286 common selective sweeps that were detected in at least two comparisons as important candidates for selection during breeding. Notably, 23.5% of our selective sweeps overlapped with previously reported sweeps for improvement in GJ rice of central China ( Xiao et al., 2021 ), indicating that the genomic regions selected during modern breeding are distinct among different rice cropping regions, potentially owing to environmental differences.

Figure 3 Whole-genome screening for differential selection during modern GJ rice breeding.

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Grain Quality Affected by Introducing Photorespiratory Bypasses into Rice

“…It has been considered that yields and quality are negatively related, although no genetic linkage has been established [43]. High quality without high yield is widely observed in crop breeding science [44,45], and many popular high-yielding cultivars and hybrids have relatively poor quality [13]. As the main staple, rice production must meet increasing demands for both quantity and quality to ensure an appropriate level of sustainability.…”

Development of Rice Variety With Durable and Broad-Spectrum Resistance to Blast Disease Through Marker-Assisted Introduction of Pigm Gene

“…Notably, a rice line YNG3091 from BC 3 F 6 generation has been authorized as a new rice variety in Jiangsu province, which displays good resistance to both seedling blast and panicle blast, as well as excellent performance on both grain yield and quality (Figure 5). Most recently, a new geng variety Jinxiangyu 1 carrying Pigm was also developed via MAS in Jiangsu province, which also showed excellent blast resistance and high yield (Xiao et al, 2021). Together, these demonstrate that Pigm has a high breeding value in developing a blastresistant variety and the reduction effect of PigmR on grain weight could be overcome by agronomical trait selection.…”