Construction of Molecular Genetic Linkage Map Based on an RIL Population of Rice and Detection of QTLs for Tiller Angle

In this study, an RIL （recombinant inbred line） population containing 240 lines was developed by single seed descent method （SSD） based on a parent com- bination of small-grain indica cultivar Kasalath and large-grain japanica cultivar TD70 with significant differences in plant type traits, to construct the molecular genetic linkage map. Totally 838 SSR （Simple Sequence Repeat） markers were used for polymorphism screening between parents, 302 SSR markers with polymorphism were detected, with a frequency of 36.04%; 141 SSR markers with clear amplified bands and uniform distribution in the genome were finally used for genotype analysis of the RIL population. According to the experimental results, the frequency of male and female genotype in this RIL population was respectively 53% and 47%, suggesting good balance in population structure. A molecular genetic linkage map of rice was constructed by 141 markers based on a RIL population of 240 lines, with a total genetic distance of about 1 832.47 cM covering all 12 chromosomes, an average genetic distance between markers of 12.70 cM and a range of genetic distance be- tween markers of 0.43-36.11 cM, which is consistent with basic requirements of quantitative trait locus （QTL） mapping. Except for few markers on chromosomes 1 and 8, the order and location of markers is similar to the published sequences of Nipponbare. QTL analysis for the tiller angle was conducted with this RIL population of 240 lines, and results showed that three QTLs controlling tiller angle were detected on chromosome 8, 9 and 11, which were named qTA8, qTA9 and qTA11, with a contribution rate of 4.10%, 26.08% and 4.35%, respectively. To be specific, qTA9 contained Tiller Angle Controlling （TAC1） gene. The construction of this molecular genetic linkage map laid the foundation for genetic analysis and QTL mapping of various traits in the progeny of indica and japonica.

PROG1 acts upstream of LAZY1 to regulate rice tiller angle as a repressor

Rice tiller angle,as a component of plant architecture,affects rice grain yield via plant density.However,the molecular mechanism underlying rice tiller angle remains elusive.We report that the key domestication gene PROSTRATE GROWTH 1(PROG1)controls rice tiller angle by regulating shoot gravitropism and LAZY1(LA1)-mediated asymmetric distribution of auxin.Acting as a transcriptional repressor,PROG1 negatively regulates the expression of LA1 in light-grown rice seedlings.Overexpression of LA1 partially rescued the larger tiller angle of the PROG1 complementation transgenic plant(prog1-D).Double-mutant analysis showed that PROG1 acts upstream of LA1 to regulate shoot gravitropism and tiller angle.Mutation of Suppressors of lazy1(SOL1),encoding DWARF3(D3)acting in the strigolactone signal pathway,suppressed the large tiller angle of prog1-D by rescuing the transcription of LA1.The discovery of a light-sensitive PROG1-LA1 transcription regulatory module controlling rice shoot gravitropism and tiller angle sheds light on the genetic control of rice tiller angle.

Genetic Analysis and Gene Mapping of a Rice Tiller Angle Mutant tac2

Tiller angle, a very essential agronomic trait, is significant in rice breeding, especially in plant type breeding. A tiller anglo controlling 2 （tac2） mutant was obtained from a restorer line Jinhui 10 by ethyl methane sulphonate mutagenesis. The tac2 mutant displayed normal phenotype at the seedling stage and the tiller angle significantly increased at the tillering stage, A preliminary physiological research indicated that the mutant was sensitive to GA. Thus, it is speculated that TAC2 and TAC1 might control the tiller angle in the same way. Genetic analysis showed that the mutant trait was controlled by a major recessive gene and was located on chromosome 9 using SSR markers. The genetic distances between TAC2 and its nearest markers RM3320 and RM201 were 19.2 cM and 16,7 cM, respectively.

The chloroplast-localized protein LTA1 regulates tiller angle and yield of rice

Plant architecture strongly influences rice grain yield.We report the cloning and characterization of the LTA1 gene,which simultaneously controls tiller angle and yield of rice.LTA1 encodes a chloroplastlocalized protein with a conserved YbaB DNA-binding domain,and is highly expressed in photosynthetic tissues including leaves and leaf sheaths.Disrupting the function of LTA1 leads to large tiller angle and yield reduction of rice.LTA1 affects the gravity response by mediating the distribution of endogenous auxin,thereby regulating the tiller angle.An lta1 mutant showed abnormal chloroplast development and decreased chlorophyll content and photosynthetic rate,in turn leading to reduction of rice yield.Our findings shed light on the genetic basis of tiller angle and provide a potential gene resource for the improvement of plant architecture and rice yield.

A major vernalization-independent QTL for tiller angle on chromosome arm 2BL in bread wheat

Tiller angle(TA)strongly influences plant architecture and grain yield in cereals.However,the genetic basis of TA in wheat is largely unknown.We identified three TA-related quantitative trait loci(QTL).One of them was QTa.sau-2 B-769,a major QTL localized on chromosome arm 2 BL.QTa.sau-2 B-769 was detected in seven environments,explaining 18.1%–51.1%of phenotypic variance.We developed a linked Kompetitive Allele-Specific Polymerase chain reaction(KASP)marker,KASP-AX-108792274,to further validate this locus in three additional populations in multiple environments.QTa.sau-2 B-769 increased TA by up to 24.9%in these populations.There were significant and positive correlations between TA and flag leaf angle(FLANG).However,TA was not correlated with plant height or anthesis date,suggesting that expression of QTa.sau-2 B-769 is independent of vernalization.Traes CS2 B01 G583800,a gene known to be involved in leaf angle regulation,was identified as the most likely candidate gene for QTa.sau-2 B-769.These results enrich our understanding of the mechanisms regulating wheat TA at maturity and may support precise mapping and cloning of gene(s)underlying QTa.sau-2 B-769.

Identification of the candidate gene controlling tiller angle in common wheat through genome-wide association study and linkage analysis

Wheat tiller angle(TA)is an important agronomic trait that contributes to grain production by affecting plant architecture.It also plays a crucial role in high-yield wheat breeding.An association panel and a recombinant inbred line(RIL)population were used to map quantitative trait loci(QTL)for TA.Results showed that 470 significant SNPs with 10.4%–28.8%phenotypic variance explained(PVE)were detected in four replicates by a genome-wide association study(GWAS).Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA.Ten QTL were totally detected by linkage mapping with the RIL population,and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%–18.82%was a major and stable QTL.A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region.Moreover,QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq(BSR-Seq)analysis.Phenotypic analysis showed that QTA.hau-4B.1was also closely related to yield traits.Furthermore,Traes CS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression.This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.

LAZY1 controls rice shoot gravitropism through regulating polar auxin transport

Tiller angle of rice （Oryza sativa L.） is an important agronomic trait that contributes to grain production, and has long attracted attentions of breeders for achieving ideal plant architecture to improve grain yield. Although enormous efforts have been made over the past decades to study mutants with extremely spreading or compact tillers, the molecular mechanism underlying the control of tiller angle of cereal crops remains unknown. Here we report the cloning of the LAZY1 （LA1） gene that regulates shoot gravitropism by which the rice tiller angle is controlled. We show that LA1, a novel grass-specific gene, is temporally and spatially expressed, and plays a negative role in polar auxin transport （PAT）. Loss-of-function of LA1 enhances PAT greatly and thus alters the endogenous IAA distribution in shoots, leading to the reduced gravitropism, and therefore the tiller-spreading phenotype of rice plants.

BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

Tiller angle is a key agricultural trait that establishes plant architecture,which in turn strongly affects grain yield by influencing planting density in rice.The shoot gravity response plays a crucial role in the regulation of tiller angle in rice,but the underlying molecular mechanism is largely unknown.Here,we report the identification of the BIG TILLER ANGLE2(BTA2),which regulates tiller angle by controlling the shoot gravity response in rice.Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base,leading to impaired gravitropism and therefore a big tiller angle.BTA2 interacted with AUXIN RESPONSE FACTOR7(ARF7)to modulate rice tiller angle through the gravity signaling pathway.The BTA2 protein was highly conserved during evolution.Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication.Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions.Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response.Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

LAZY4 acts additively with the starch-statolithdependent gravity-sensing pathway to regulate shoot gravitropism and tiller angle in rice

Rice tiller angle is a key agronomic trait that has significant effects on the establishment of a high-yield rice population.However,the molecular mechanism underlying the control of rice tiller angle remains to be clarified.Here,we characterized the novel tiller-angle gene LAZY4(LA4)in rice through map-based cloning.LA4 encodes a C3H2C3-type RING zinc-finger E3 ligase localized in the nucleus,and an in vitro ubiquitination assay revealed that the conserved RING finger domain is essential for its E3 ligase activity.We found that expression of LA4 can be induced by gravistimulation and that loss of LA4 function leads to defective shoot gravitropism caused by impaired asymmetric auxin redistribution upon gravistimulation.Genetic analysis demonstrated that LA4 acts in a distinct pathway from the starch biosynthesis regulators LA2 and LA3,which function in the starch-statolith-dependent pathway.Further genetic analysis showed that LA4 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport upon gravistimulation.Our studies reveal that LA4 regulates shoot gravitropism and tiller angle upstream of LA1 through a novel pathway independent of the LA2-LA3-mediated gravity-sensing mechanism,providing new insights into the rice tiller-angle regulatory network.

Molecular basis underlying rice tiller angle:Current progress and future perspectives

Crop plant architecture is an important agronomic trait that contributes greatly to crop yield.Tiller angle is one of the most critical components that determine crop plant architecture,which in turn substantially af-fects grain yield mainly owing to its large influence on plant density.Gravity is a fundamental physical force that acts on all organisms on earth.Plant organs sense gravity to control their growth orientation,including tiller angle in rice(Oryza sativa).This review summarizes recent research advances made using rice tiller angle as a research model,providing insights into domestication of rice tiller angle,genetic regulation of rice tiller angle,and shoot gravitropism.Finally,we propose that current discoveries in rice can shed light on shoot gravitropism and improvement of plant tiller/branch angle in other species,thereby contributing to agricultural production in the future.