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Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement. To investigate its molecular mechanisms in rice, we performed map-based cloning and characterization of OPEN PANICLE 1 (OP1), a gain-of-function allele of LIGULELESS 1 (LG1), controlling the spread-panicle phenotype. This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch. Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1 (sp1). Knocking out BRASSINOSTEROID UPREGULATED1 (BU1) gene in the background of OP1 complementary plants resulted in compact panicles, suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway. We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture. [ABSTRACT FROM AUTHOR]

Doubled haploid (DH) technology is an important tool in crop breeding because it can significantly accelerate the breeding process. ZmPLA1/MATL/NLD and ZmDMP are two key genes controlling haploid induction (HI) in maize, exhibiting a synergistic effect. However, it is unknown whether knock out of ZmDMP orthologs can stimulate HI in rice. In this study, a ZmPLA1 ortholog (OsPLA1) and two ZmDMP orthologs (OsDMP3 and OsDMP6) were identified in rice. All three genes encode plasma membrane-localized proteins and were highly expressed in mature anthers. Knockout of OsPLA1 in both Minghui 63 and Nipponbare resulted in reduced seed setting rate (SSR) and caused HI. The osdmp3, osdmp6 and the double mutant failed to trigger HI independently, nor increased the haploid induction rate (HIR) when combined with ospla1. Repeated pollinations operations of QX654A with the ospla1 mutant significantly improve SSR, while reducing HIR. RNA-seq profiling of mature ospla1 mutant anthers indicated that a large number of differentially expressed genes (DEGs) were enriched in redox homeostasis and lipid metabolic GO terms, plant hormone signal transduction, and MAPK signaling pathways. These findings provide important insights towards construction of an efficient DH breeding technology and study of the molecular mechanism of HI in rice. [ABSTRACT FROM AUTHOR]

During rice domestication and improvement, increasing grain yield to meet human needs was the primary objective. Rice grain yield is a quantitative trait determined by multiple genes, but the molecular basis for increased grain yield is still unclear. Here, we show that NUMBER OF GRAINS 1 (NOG1), which encodes an enoyl-CoA hydratase/isomerase, increases the grain yield of rice by enhancing grain number per panicle without a negative effect on the number of panicles per plant or grain weight. NOG1 can significantly increase the grain yield of commercial high-yield varieties: introduction of NOG1 increases the grain yield by 25.8% in the NOG1-deficient rice cultivar Zhonghua 17, and overexpression of NOG1 can further increase the grain yield by 19.5% in the NOG1-containing variety Teqing. Interestingly, NOG1 plays a prominent role in increasing grain number, but does not change heading date or seed-setting rate. Our findings suggest that NOG1 could be used to increase rice production. [ABSTRACT FROM AUTHOR]

A molecular linkage map was developed for the tetraploid orchardgrass ( Dactylis glomerata L.) from an F1 pseudo-testcross population of 76 individuals derived from the cross between two individual plants of Akimidori, a Japanese cultivar and Loke, a Swedish cultivar. Two simple sequence repeat (SSR)-based parental linkage maps were constructed from 314 polymorphic homologous SSR markers derived from the same species. The Akimidori map consisted of 24 linkage groups (LGs) and had a total length of 562 cM, with 168 loci and an average map density of 3.3 cM. Five homologous LGs were detected on this map. The Loke map consisted of 26 LGs and had a total length of 745 cM, with 227 loci and an average map density of 3.3 cM. Seven homologous LGs were detected on this map. A consensus map with seven homologous LGs was developed from these using TetraploidMap software based on the double-simplex (segregated as 3:1) and duplex (segregated as 5:1) markers. This is the first linkage map of the tetraploid Dactlysis and these maps will be useful for quantitative trait locus (QTL) analysis, marker-assisted selection and breeding for important traits in orchardgrass in the future. [ABSTRACT FROM AUTHOR]

There are few reports of the patterns of polymorphism in the non-coding regions of plant genomes. In this study, we explored nucleotide diversity and linkage disequilibrium (LD) in 47 non-coding regions on chromosome 4 of wild and cultivated rice. The cultivated rice retained about 70% of the diversity of wild rice, which was verified by coalescent simulations with one population bottleneck for 198 combinations of duration and population sizes. Multi-locus likelihood analysis showed that the severity of the bottleneck ranged from 2.25 to 3.33, with an average value of 2.70; i.e., the diversity found in the cultivated rice could be explained by a founding population of 2,700 individuals if the initial domestication event occurred over a period of 1,000 years. LD decreased more rapidly in wild rice than in cultivated rice within 10 kb, and the LD observed in cultivated rice was increased at 100–140 kb by comparison with wild rice. The patterns of LD indicated the possibility of a haplotype block in cultivated rice but not in wild rice. [ABSTRACT FROM AUTHOR]

To understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a BC3F2 population derived from an accession of common wild rice (donor, Oryza rufipogon Griff.) collected from Yuanjiang, Yunnan province, China, and an indica cultivar, Teqing (recipient, Oryza sativa L.). A genetic linkage map consisting of 125 simple sequence repeat (SSR) markers was constructed. Based on the phenotypes of the 383 BC3F2 families evaluated in two environments, two domestication-related morphological traits, panicle shape and growth habit, were found to be controlled by single Mendelian factors. This implies that the recessive mutations of single genes controlling some morphological traits could have been easily selected during early domestication. By single-point analysis and interval mapping, 59 putative quantitative trait loci (QTLs) that influence 11 quantitative traits were detected at two sites, and 37.5% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield-related traits in the Teqing background. Regions with significant QTLs for domestication- and yield-related traits were detected on chromosomes 1, 4, 5, 7, 8, and 12. Fine mapping and cloning of these domestication-related genes and QTLs will be useful in elucidating the origin and differentiation of Asian cultivated rice in the future. Afin de mieux comprendre les propriétés génétiques des caractères liés à la différenciation entre le riz cultivé et son ancêtre sauvage, les facteurs génétiques contrôlant les caractères liés à la domestication et au rendement ont été identifiés au sein d’une population BC3F2 dérivée du croisement entre une accession du riz sauvage commun (Oryza rufipogon Griff., parent mâle) provenant de Yuanjiang (province du Yunnan en Chine) et le cultivar Teqing de type indica (Oryza sativa L., parent femelle). Une carte génétique comprenant 125 marqueurs microsatellites (SSR) a été produite. Sur la base des phénotypes observés chez 383 familles BC3F2 évaluées dans deux environnements, il a été trouvé que deux caractères morphologiques liés à la domestication, la forme de la panicule et le port de la plante, étaient contrôlés par des facteurs mendéliens uniques. Ceci implique qu’il aurait été facile de sélectionner les mutations récessives pour certains caractères morphologiques contrôlés par des gènes uniques lors de la domestication. En employant des analyses ponctuelles et par intervalles, 59 QTL putatifs contrôlant 11 caractères quantitatifs ont été détectés sur les deux sites. Dans ces cas, 37,5 % des allèles de l’O. rufipogon avaient des effets positifs sur des composantes du rendement dans un fond génétique Teqing. Des régions portant des QTL significatifs pour les caractères liés à la domestication ou au rendement ont été détectées sur les chromosomes 1, 4, 5, 7, 8 et 12. La cartographie fine et le clonage de ces gènes et QTL liés à la domestication seront utiles dans le futur pour élucider l’origine et la différenciation du riz cultivé asiatique. [ABSTRACT FROM AUTHOR]

As a prerequisite for the map-based cloning of genes from common wild rice ( Oryza rufipogon Griff.), which plays an important role in the domestication of cultivated rice ( O. sativa L.), we constructed a median-insert size bacterial artificial chromosome (BAC) library of the common wild rice isolate, YJCWR, collected from Yuanjiang, Yunnan Province, China. The library consists of 52,992 clones, with an average insert size of 50 kb, and all clones were pooled into 46 three-dimensional super-pools to facilitate library screening through the PCR method. Seventeen candidate clones were isolated by five markers and some clones containing putative target regions were sequenced. Furthermore, in analyzing the sequences of YJCWR, a retrotransposon, SZ-55, that might contribute to the evolution of Oryza was found. [ABSTRACT FROM AUTHOR]

A critical step during rice ( Oryza sativa) cultivation is dense planting: a wider tiller angle will increase leaf shade and decrease photosynthesis efficiency, whereas a narrower tiller angle makes for more efficient plant architecture. The molecular basis of tiller angle remains unknown. This research demonstrates that tiller angle is controlled by a major quantitative trait locus, TAC1 ( Tiller Angle Control 1). TAC1 was mapped to a 35-kb region on chromosome 9 using a large F2 population from crosses between an indica rice, IR24, which displays a relatively spread-out plant architecture, and an introgressed line, IL55, derived from japonica rice Asominori, which displays a compact plant architecture with extremely erect tillers. Genetic complementation further identified the TAC1 gene, which harbors three introns in its coding region and a fourth 1.5-kb intron in the 3′-untranslated region. A mutation in the 3′-splicing site of this 1.5-kb intron from ‘AGGA’ to ‘GGGA’ decreases the level of tac1, resulting in a compact plant architecture with a tiller angle close to zero. Further sequence verification of the mutation in the 3′-splicing site of the 1.5-kb intron revealed that the tac1 mutation ‘GGGA’ was present in 88 compact japonica rice accessions and TAC1 with ‘AGGA’ was present in 21 wild rice accessions and 43 indica rice accessions, all with the spread-out form, indicating that tac1 had been extensively utilized in densely planted rice grown in high-latitude temperate areas and at high altitudes where japonica rice varieties are widely cultivated. [ABSTRACT FROM AUTHOR]

Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing ( O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teging background. These O. rufipogon -O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice. [ABSTRACT FROM AUTHOR]

A critical evolutionary step during rice domestication was the elimination of seed shattering. Wild rice disperses seeds freely at maturity to guarantee the propagation, while cultivated rice retains seeds on the straws to make easy harvest and decrease the loss of production. The molecular basis for this key event during rice domestication remains to be elucidated. Here we show that the seed shattering is controlled by a single dominant gene, Shattering1 ( SHA1), encoding a member of the trihelix family of plant-specific transcription factors. SHA1 was mapped to a 5.5 kb genomic fragment, which contains a single open reading frame, using a backcrossed population between cultivated rice Teqing and an introgression line IL105 with the seed shattering habit derived from perennial common wild rice, YJCWR. The predicted amino acid sequence of SHA1 in YJCWR and IL105 is distinguished from that in eight domesticated rice cultivars, including Teqing, by only a single amino acid substitution (K79N) caused by a single nucleotide change (g237t). Further sequence verification on the g237t mutation site revealed that the g237t mutation is present in all the domesticated rice cultivars, including 92 indica and 108 japonica cultivars, but not in any of the 24 wild rice accessions examined. Our results demonstrate that the g237t mutation in SHA1 accounts for the elimination of seed shattering, and that all the domesticated rice cultivars harbor the mutant sha1 gene and therefore have lost the ability to shed their seeds at maturity. In addition, our data support the theory that the non-shattering trait selection during rice domestication occurred prior to the indica– japonica differentiation in rice evolutionary history. [ABSTRACT FROM AUTHOR]

SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F2 and F3 generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F2 plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F3 families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle. [ABSTRACT FROM AUTHOR]