Zhengjin Xu

Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China.

Rice is one of mankind’s major food staples, and the erect panicle architecture in rice is an important morphological improvement. The dense and erect panicle 1 (DEP1) locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity of DEP1 remains narrow. In order to improve the genetic diversity of DEP1, we used a rice germplasm collection of 72 high yielding japonica rice varieties to analyze the contribution of DEP1 to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of DEP1. We further detected 7 haplotypes and found that the replacement of 637 bp by a 12 bp fragment could explain the erect panicle architecture in all 72 germplasms. An SNP (G/C) at the -1253 bp of the promoter region caused a core sequence shift (TGGGCC) of a site II transcriptional regulatory element. The association analysis showed that the SNP(G/C) largely affects the number of primary and secondary branches, and grain number per panicle. Our results provide novel insights into the function and genetic diversity of DEP1. The SNP (G/C) at the promoter region will contribute to the flexible application of DEP1 in rice breeding.

Different effects of DEP1 on vascular bundle- and panicle-related traits under indica and japonica genetic backgrounds

Rice (Oryza sativa L.) is a major food for more than half of the world’s population and serves as a model monocot plant. DEP1 (dense and erect panicle 1), corresponding to an erect-panicle architecture, may bring the third breakthrough in rice breeding after the introduction of the semi-dwarf trait and the application of heterosis in hybrid rice. The aim of this study was to determine the effects of DEP1 on yield components and vascular bundle-related traits under indica and japonica genetic backgrounds. We analyzed a series of recombinant inbred lines, which were derived from a cross between the japonica variety SN265 with an erect panicle and the indica variety R99 with a curved panicle. The results showed that effects of the DEP1/dep1 allele were much stronger than the effects of the indica/japonica genetic background on vascular bundle-related traits and yield components. As the frequency of indica alleles increased, the grain yield per plant and the harvest index significantly increased in lines with the dep1 allele. Among the indica-type lines, those with the dep1 allele showed superior values for almost all of the vascular bundle-related traits and yield components. Our results provide new insights into the use of a high-yield-related gene derived from japonica in the indica genetic background.

Relationship between grain yield and quality in rice germplasms grown across different growing areas.

Rice grain yield and quality are two major foci of rice breeding. In this study, Chinese regional rice test data provide us the unique opportunity to analyze the relationship between yield and quality in rice, because China has an unusually wide range of rice cultivars. We analyzed the relationships between grain yield, yield components, and grain quality of 300 rice germplasms. Japonica was superior in both yield and quality compared with indica. A high setting rate improved the head rice ratio. A higher 1000 grain weight was negatively correlated with quality characteristics but had a positive correlation with yield. A high spikelet density (number of grains per centimeter on the panicle) not only benefits the yield but also the head rice ratio and chalkiness traits. According to our results, global rice production can be increased to at least 8500 kg/ha to meet projected demands in 2025 without sacrificing grain quality.

The DENSE AND ERECT PANICLE 1 (DEP1) gene offering the potential in the breeding of high-yielding rice

The erect panicle model super-rice can rationally transform the solar energy into accumulated organic matter (biomass) and increase grain yield. The phenotype of erect panicle architecture controlled by DENSE AND ERECT PANICLE 1 (DEP1) has been used in rice breeding for nearly a century owing to its high-yield, lodging tolerance with strong stem, reasonable population structure and high nitrogen use efficiency. DEP1 is a G protein γ subunit that is involved in the regulation of erect panicle, number of grains per panicle, nitrogen uptake, and stress-tolerance through the G protein signal pathway. Here we review the development of erect panicle rice varieties, DEP1 alleles and regulatory network, and its physiological and morphological functions. Additionally, the further increasing the yield potential of erect-panicle super-rice, and the development of molecular designing breeding for indica-japonica hybrid rice with the dep1 gene are also prospected.

Characterization and fine mapping of thermo-sensitive chlorophyll deficit mutant1 in rice (Oryza sativa L.)

Chlorophyll content is one of the most important traits controlling crop biomass and economic yield in rice. Here, we isolated a spontaneous rice mutant named thermo-sensitive chlorophyll deficit 1 (tscd1) derived from a backcross recombinant inbred line population. tscd1 plants grown normally from the seedling to tiller stages showed yellow leaves with reduced chlorophyll content, but showed no significant differences after the booting stage. At temperatures below 22°C, the tscd1 mutant showed the most obvious yellowish phenotype. With increasing temperature, the yellowish leaves gradually turned green and approached a normal wild type color. Wild type and tscd1 mutant plants had obviously different chloroplast structures and photosynthetic pigment precursor contents, which resulted in underdevelopment of chloroplasts and a yellowish phenotype in tscd1. Genetic analysis indicated that the mutant character was controlled by a recessive nuclear gene. Through map-based cloning, we located the tscd1 gene in a 34.95 kb region on the long arm of chromosome 2, containing two BAC clones and eight predicted candidate genes. Further characterization of the tscd1 gene is underway. Because it has a chlorophyll deficit phenotype before the tiller stage and little influence on growth vigor, it may play a role in ensuring the purity of hybrids.

Response of the leaf photosynthetic rate to available nitrogen in erect panicle-type rice (Oryza sativa L.) cultivar, Shennong265

Abstract Increasing the yield of rice per unit area is important because of the demand from the growing human population in Asia. A group of varieties called erect panicle-type rice (EP) achieves very high yields under conditions of high nitrogen availability. Little is known, however, regarding the leaf photosynthetic capacity of EP, which may be one of the physiological causes of high yield. We analyzed the factors contributing to leaf photosynthetic rate (Pn) and leaf mesophyll anatomy of Nipponbare, Takanari, and Shennong265 (a EP type rice cultivar) varieties subjected to different nitrogen treatments. In the field experiment, Pn of Shennong265 was 33.8 μmol m−2 s−1 in the high-N treatment, and was higher than that of the other two cultivars because of its high leaf nitrogen content (LNC) and a large number of mesophyll cells between the small vascular bundles per unit length. In Takanari, the relatively high value of Pn (31.5 μmol m−2 s−1) was caused by the high stomatal conductance (gs; .72 mol m−2 s−1) in the high-N treatment. In the pot experiment, the ratio of Pn/Ci to LNC, which may reflect mesophyll conductance (gm), was 20–30% higher in Nipponbare than in Takanari or Shennong265 in the high N availability treatment. The photosynthetic performance of Shennong265 might be improved by introducing the greater ratio of Pn/Ci to LNC found in Nipponbare and greater stomatal conductance found in Takanari.

Yield and growth characteristics of erect panicle type rice (Oryza sativa L.) cultivar, Shennong265 under various crop management practices in Western Japan

Abstract Erect panicle rice cultivars utilize solar energy effectively and have improved ecological growing conditions. Among such cultivars, Shennong265 has been grown successfully throughout Northern China. Nevertheless, no studies have yet examined the relationships between crop dry matter productivity, weather conditions, and nitrogen uptake of the erect panicle type rice cultivar in Japan. The objective of our study was to evaluate the productivity of erect panicle rice Shennong265 in Western Japan under varied conditions. Three rice cultivars, Shennong265, Nipponbare, and Takanari were grown in the field under different fertilizer and plant density conditions in Western Japan; using this information, we compared yield and growth characteristics of Shennong265 with those of Nipponbare and Takanari. Although Shennong265 had radiation use efficiency similar to that of the high yielding cultivar (Takanari) and much higher leaf nitrogen content than Takanari and Nipponbare, the average grain yield of Shennong265 grown under normal fertilizer and plant density conditions was approximately 6.9 t ha−1 as against 6.2 t ha−1 for Nipponbare and 9.6 t ha−1 for Takanari. These results suggest that, while Shennong265 has a high yield potential, the environmental conditions including climate, fertilizer, and planting period provided in this study were not suitable for achieving its maximum yield. The reduced performance of Shennong265 may be caused by insufficient fertilizer after heading and by shorter growth periods, as well as by the climate of Western Japan. Additional fertilizer application during the heading stage and earlier transplanting may be needed to obtain higher Shennong265 yields in Western Japan.

Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

BackgroundTwo of the most widely cultivated rice strains are Oryza sativa indica and O. sativa japonica, and understanding the genetic basis of their agronomic traits is of importance for crop production. These two species are highly distinct in terms of geographical distribution and morphological traits. However, the relationship among genetic background, ecological conditions, and agronomic traits is unclear.ResultsIn this study, we performed the de novo assembly of a high-quality genome of SN265, a cultivar that is extensively cultivated as a backbone japonica parent in northern China, using single-molecule sequencing. Recombinant inbred lines (RILs) derived from a cross between SN265 and R99 (indica) were re-sequenced and cultivated in three distinct ecological conditions. We identify 79 QTLs related to 15 agronomic traits. We found that several genes underwent functional alterations when the ecological conditions were changed, and some alleles exhibited contracted responses to different genetic backgrounds. We validated the involvement of one candidate gene, DEP1, in determining panicle length, using CRISPR/Cas9 gene editing.ConclusionsThis study provides information on the suitable environmental conditions, and genetic background, for functional genes in rice breeding. Moreover, the public availability of the reference genome of northern japonica SN265 provides a valuable resource for plant biologists and the genetic improvement of crops.

Recombination between DEP1 and NRT1.1B under japonica and indica genetic backgrounds to improve grain yield in rice

DEP1 and NRT1.1B genes for improving nitrogen utilization efficiency (NUE) have been widely used in japonica and indica rice (Oryza sativa L.) breeding, respectively. The aim of this study was to determine the effect of the non-allelic recombination of two genes on agronomic traits, grain yield and NUE under japonica and indica genetic backgrounds. One hundred and fifty-one recombinant inbred lines were derived from a cross between japonica variety SN265 with dep1/NRT1.1B alleles and indica variety R99 with DEP1/nrt1.1b alleles. Among these, we found four genotypes (DEP1/NRT1.1B, DEP1/nrt1.1b, dep1/NRT1.1B and dep1/nrt1.1b) under japonica and indica genetic backgrounds. Results showed a significant increase in nitrate reductase activity, N uptake and grain yield under low N growth condition, after the nrt1.1b allele was introduced into japonica lines with dep1. Whereas, the introduction of dep1 allele into indica lines with nrt1.1b increased glutamine synthetase activity, N transfer and grain yield under both low and high N growth conditions. Our results showed diverse physiological pathway between dep1 and nrt1.1b alleles in the N metabolism of rice, providing new strategies in flexible application of dep1 and nrt1.1b alleles for improvement of NUE in japonica and indica rice breeding.

Effect of indica pedigree on eating and cooking quality in rice backcross inbred lines of indica and japonica crosses

Amylopectin is one of the major determinants of rice (Oryza sativa L.) grain quality, and a large difference in amylopectin is found between two subspecies: japonica and indica. However, the relationship among rice grain quality, indica/japonica genetic background, and amylopectin has not been clearly established. In this study, a series of backcross inbred lines derived from the cross between japonica (cv. Sasanishiki) and indica (cv. Habataki) were used to survey eating and cooking quality (ECQ), rapid visco analyzer (RVA) profiles, and the chain length distribution of amylopectin. The frequency of indica pedigree (Fi) was calculated to analyze the effects of Fi on grain quality and amylopectin. The results showed that the Sasanishiki cultivar was markedly enriched in chain length with DP6-15 and DP34-45 compared to the Habataki. DP34-45 strongly correlated to RVA characteristics, cooking quality, and prolamin content. The Fi also has significant correlations to RVA characteristics and ECQ, but only significantly negative correlation to DP34-45. Seven quantitative trait loci (QTLs) corresponding to amylopectin were mapped, of which three were in agreement with previous findings. The results of this study provide valuable information for amylopectin characteristics in the offspring derived from the subspecies cross, and the novel QTLs may provide new insights to the identification of minor starch synthesis-related genes.