Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China.

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.

Transcriptomic profiling of the cold stress and recovery responsiveness of two contrasting Guizhou HE rice genotypes.

BACKGROUND: At the seed germination stage, rice is sensitive to cold stress, which adversely affects its growth and development. Guizhou HE rice comprises several different landraces, most of which are cold tolerant. OBJECTIVE: To identify differentially expressed genes and molecular mechanism underlying the cold tolerance of Guizhou HE. METHODS: Two Guizhou HE genotypes, AC44 (cold-sensitive) and AC96 (cold-tolerant), which exhibit opposite phenotypes in response to cold treatment at the seed germination stage were used. Comprehensive gene expressions of AC44 and AC96 under 4 °C cold treatment and subsequent recovery conditions were comparatively analyzed by RNA sequencing. RESULTS: Overall, 11,082 and 7749 differentially expressed genes were detected in AC44 and AC96, respectively. Comparative transcriptome analysis demonstrated that, compared with AC44, AC96 presented fewer upregulated and downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that AC96 presented more upregulated GO terms, especially terms associated with biological processes. However, AC44 presented more terms related to cellular components, mainly chloroplasts. Moreover, DEGs related to the auxin signaling pathway (including ARF and IAA family members) and transcription factors (including members of the F-box, bZIP, basic helix-loop-helix [bHLH], and MYB-like transcription factor families) were found to be expressed specifically in AC96; thus, these DEGs may be responsible for the cold tolerance of AC96. CONCLUSIONS: These findings present information about the cold tolerance mechanism of Guizhou HE rice at the germination stage, providing valuable resources and candidate genes for breeding cold-tolerant rice genotypes.

Transcriptome analysis of floret opening and closure both Indica and Japonica rice.

Floret opening and closure are critical for rice to complete reproductive development. To further understand the molecular mechanism of floret opening and closure in rice, RNA-seq was performed on the floret of Indica and Japonica rice in the state of 1-h before floret opening, at the opening and closure, respectively. Our results show that many differentially expressed genes are produced throughout the floret opening and closure of both Indica and Japonica rice. Differentially expressed genes shared between Indica and Japonica rice at floret opening were involved in seven metabolic pathways, including plant hormone signal transduction, MAPK signaling pathway-plant, starch and sucrose metabolism, alpha-Linolenic acid metabolism, plant-pathogen interaction, diterpenoid biosynthesis, glucuronate interconversions, phenylpropanoid biosynthesis, compared to 1 h before floret opening. In addition, the expression patterns of some genes, OsJAZ13, OsJAZ11 and OsCML1 which the above metabolic pathways, were different between Indica and Japonica rice. Compared to the floret opening, the differentially expressed genes at floret closure were mainly involved in the following three metabolic pathways: Circadian rhythm-plant, sesquiterpenoid and triterpenoid biosynthesis, starch and sucrose metabolism, and thiamine metabolism. This study provides insights into revealing the molecular mechanism of floret opening and closure in rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03226-y.

Genetic mapping of powdery mildew resistance genes in wheat landrace Guizi 1 via genotyping by sequencing.

BACKGROUND: Wheat (Triticum aestivum L.) powdery mildew (Pm), which caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease worldwide that causes severe yield losses in wheat. Resistant wheat cultivars easily lose their ability to effectively resist newly emerged Bgt strains; therefore, identifying new resistance genes is necessary for breeding resistant cultivars. METHODS AND RESULTS: Guizi 1 (GZ1) is a Chinese wheat cultivar with moderate and stable resistance to Pm. Genetic analysis indicated that the Pm resistance of GZ1 was controlled by a single dominant gene, designated PmGZ1. In total, 110 F2 individual plants and their 2 parents were subjected to genotyping by sequencing (GBS), which yielded 23,134 high-quality single-nucleotide polymorphisms (SNPs). The SNP distributions across the 21 chromosomes ranged from 134 on chromosome 6D to 6288 on chromosome 3B. Chromosome 6A has 1866 SNPs, among which 16 are physically located between positions 307,802,221 and 309,885,836 in an approximate 2.3-cM region; this region also had the greatest SNP density. The average map distance between SNP markers was 0.1 cM. A quantitative trait locus (QTL) with a significant epistatic effect on Pm resistance was mapped to chromosome 6A. The logarithm of odds (LOD) value of PmGZ1 was 34.8, and PmGZ1 was located within the confidence interval marked by chr6a-307802221 and chr6a-309885836. Moreover, 74.7% of the phenotypic variance was explained by PmGZ1. Four candidate genes (which encoded two TaAP2-A and two actin proteins) were annotated maybe as resistance genes. CONCLUSIONS: The present results provide valuable information for wheat genetic improvement, QTL fine mapping, and candidate gene validation.

From Green Super Rice to green agriculture: Reaping the promise of functional genomics research.

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.

FLOURY SHRUNKEN ENDOSPERM1 Connects Phospholipid Metabolism and Amyloplast Development in Rice.

Starch synthesized and stored in amyloplasts serves as the major energy storage molecule in cereal endosperm. To elucidate the molecular mechanisms underlying amyloplast development and starch synthesis, we isolated a series of floury endosperm mutants in rice (Oryza sativa). We identified the rice mutant floury shrunken endosperm1 (fse1), which exhibited obvious defects in the development of compound starch grains, decreased starch content, and altered starch physicochemical features. Map-based cloning showed that FSE1 encodes a phospholipase-like protein homologous to phosphatidic acid-preferring phospholipase A1FSE1 was expressed ubiquitously with abundant levels observed in developing seeds and roots. FSE1 was localized to both the cytosol and intracellular membranes. Lipid profiling indicated that total extra-plastidic lipids and phosphatidic acid were increased in fse1 plants, suggesting that FSE1 may exhibit in vivo phospholipase A1 activity on phosphatidylcholine, phosphatidylinositol, phosphatidyl-Ser, phosphatidylethanolamine, and, in particular, phosphatidic acid. Additionally, the total galactolipid content in developing fse1 endosperm was significantly reduced, which may cause abnormal amyloplast development. Our results identify FSE1 as a phospholipase-like protein that controls the synthesis of galactolipids in rice endosperm and provide a novel connection between lipid metabolism and starch synthesis in rice grains during endosperm development.

Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross.

The size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size (e.g., length and width) when breeding novel rice varieties. It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In the present study, a population of recombinant inbred lines (RILs) and reciprocal single chromosomal segment substitution lines (SSSLs) derived from the progeny of a japonica Asominori × indica IR24 cross were grown under four diverse environmental conditions. Six morphological traits associated with leaf size were measured, namely length and flag leaf, length and flag, second and third leaves. In the RIL population, 49 QTLs were identified that clustered in 30 genomic region. Twenty-three of these QTLs were confirmed in the SSSL population. A comparison with previously reported genes/QTLs revealed eight novel genomic regions that contained uncharacterized ORFs associated with leaf size. The QTLs identified in this study can be used for marker-assisted breeding and for fine mapping of novel genetic elements controlling leaf size in rice.

The vacuolar processing enzyme OsVPE1 is required for efficient glutelin processing in rice.

Rice (Oryza sativa L.) accumulates prolamines and glutelins as its major storage proteins. Glutelins are synthesized on rough endoplasmic reticulum as 57-kDa precursors; they are then sorted into protein storage vacuoles where they are processed into acidic and basic subunits. We report a novel rice glutelin mutant, W379, which accumulates higher levels of the 57-kDa glutelin precursor. Genetic analysis revealed that the W379 phenotype is controlled by a single recessive nuclear gene. Using a map-based cloning strategy, we identified this gene, OsVPE1, which is a homolog of the Arabidopsis betaVPE gene. OsVPE1 encodes a 497-amino-acid polypeptide. Nucleotide sequence analysis revealed a missense mutation in W379 that changes Cys269 to Gly. Like the wild-type protein, the mutant protein is sorted into vacuoles; however, the enzymatic activity of the mutant OsVPE1 is almost completely eliminated. Further, we show that OsVPE1 is incorrectly cleaved, resulting in a mature protein that is smaller than the wild-type mature protein. Taken together, these results demonstrate that OsVPE1 is a cysteine protease that plays a crucial role in the maturation of rice glutelins. Further, OsVPE1 Cys269 is a key residue for maintaining the Asn-specific cleavage activity of OsVPE1.

Fine mapping of S32(t), a new gene causing hybrid embryo sac sterility in a Chinese landrace rice (Oryza sativa L.).

Ketan Nangka, the donor of wide compatibility genes, showed sterility when crossed to Tuanguzao, a landrace rice from Yunnan province, China. Genetic and cytological analyses revealed that the semi-sterility was primarily caused by partial abortion of the embryo sac. Genome-wide analysis of the linkage map constructed from the backcross population of Tuanguzao/Ketan Nangka//Ketan Nangka identified two independent loci responsible for the hybrid sterility located on chromosomes 2 and 5, which explained 18.6 and 20.1% of phenotypic variance, respectively. The gene on chromosome 5 mapped to the previously reported sterility gene S31(t), while the gene on chromosome 2, a new hybrid sterility gene, was tentatively designated as S32(t). The BC1F2 was developed for further confirmation and fine mapping of S32(t). The gene S32(t) was precisely mapped to the same region as that detected in the BC1F1 but its position was narrowed down to an interval of about 1.9 cM between markers RM236 and RM12475. By assaying the recombinant events in the BC1F2, S32(t) was further narrowed down to a 64 kb region on the same PAC clone. Sequence analysis of this fragment revealed seven predicted open reading frames, four of which encoded known proteins and three encoded putative proteins. Further analyses showed that wide-compatibility variety Dular had neutral alleles at loci S31(t) and S32(t) that can overcome the sterilities caused by these two genes. These results are useful for map-based cloning of S32(t) and for marker-assisted transferring of the neutral allele in hybrid rice breeding.

[Genomic imprinting and seed development].

The endosperm, a seed tissue that mediates the transfer of nutrients from the maternal parent to the embryo, is an important site of imprinting in flowering plants. In Arabidopsis thaliana, three genes were identified that prevent fertilization-independent seed development: FIS1/MEDEA, FIS2 and FIS3/FIE. MEDEA (MEA), a master regulator of endosperm development, is known to be imprinted in the endosperm. FWA is also imprinted in the endosperm of the model plant Arabidopsis. The following aspects were included in the present review: the imprinting mechanism in angiosperms, the latest progress in the control of MEA and FWA imprinting, the parental conflict theory to explain imprinting, the imprinting methods and other imprinted genes found in plants.

[Screening and genetic analysis of rice glutelin mutant].

The contribution of rice as a protein source is important. Rice seed protein can be divided into four forms, glutelin (57 kDa, 37-39 kDa, 22-23 kDa), prolamine (13 kDa), albumin (16 kDa) and globulin (10 kDa, 26 kDa) on its solubility. Glutelin is the major storage protein of rice and accounted for 80% of total protein found in the rice grain, the mature glutelin comprises an acidic (37-39 kDa) and an basic subunit (22-23 kDa) coming from a common precursor (57 kDa) by post-transcriptional hydrolytic cleavage. Prolamine is the second important. Rice seed proteins localize in two types of protein bodies, PB-I, PB-II. PB-I containing prolamine is indigestible, whereas PB-II being rich in glutelin is digestible. The nutritional value of rice could thus be raised by improving its digestible protein glutelin content. On the other hand, the character of low digestible protein is also an important target of rice breeding. Low protein rice is required for the diet of patients with kidney disease. Three glutelin mutants, W3660, W204, W379, were found by screening 168 rice varieties through SDS-PAGE analysis of the seeds total proteins. The amounts of 37-39 kDa and 22-23 kDa glutelin subunits were much lower and that of 13 kDa prolamine polypeptide was higher in W3660 seeds than in ordinary rice; The amounts of 37-39 kDa and 22-23 kDa glutelin subunits in W204 or W379 seeds were between those in W3660 and ordinary rice. Especially, in W379 seed, there was a large quantity of 57 kDa polypeptide. For characterizing the genetics of the glutelin mutant, the cross population between W3660 and Otorokimochi was constructed. SDS-PAGE analysis of the progeny seed total proteins showed, low glutelin content was always accompanied by high prolamine content; all F1 seeds had low glutelin and high prolamine content; the segregation of low glutelin and normal type in F2 seeds was 3:1; the genotypes of F2 plants were deduced by the analysis of F3 seeds, and among F2 plants the ratio of homozygotes of low glutelin, heterozygotes of low glutelin and homozygotes of normal type was about 1:2:1. These results proved that the trait of low glutelin and high prolamine was controlled by a single dominant gene and could be inherited by its progeny.