Genetic and QTL analysis of maize tassel and ear inflorescence architecture

Maize (Zea mays L.) ear inflorescence architecture is directly relevant to grain yield components, and tassel architecture is relevant to hybrid seed production. The objectives of this study were to (1) determine heritabilities and correlations of a comprehensive set of tassel and ear inflorescence architecture traits in a set of (Illinois Low Protein×B73) B73 S₁ families, (2) identify chromosomal positions of QTL affecting tassel and ear architecture, and (3) identify possible candidate genes associated with these QTL. For tassel traits, the number of detected QTL ranged from one to five, and explained between 6.5 and 35.9% of phenotypic variation. For ear traits, the number of detected QTL ranged from one to nine and phenotypic variation explained by those QTL varied between 7.9 and 53.0%. We detected QTL for tassel architecture traits that required calculation of ratios from measured traits. Some of these calculated traits QTL were detected in regions that did not show QTL for the measured traits, suggesting that calculation of ratios may reveal developmentally relevant patterns of tassel architecture. We detected a QTL on chromosome 7 for tassel branch number near the gene ramosa1 (ra1), which is known to control tassel branch number, making ra1 a candidate gene for tassel branch number. We detected QTL for several traits on chromosomes 6, 8, and 9, where no inflorescence architecture genes have been mapped, thus providing initial information towards new gene discovery for control of inflorescence architecture.     

控制玉米雄穗分枝数目和雄穗重的主效QTL的定位

利用2套具有共同亲本黄早四且分别含有230个及235个家系的F_2:3群体, 结合2年多点的表型鉴定, 运用完备复合区间作图方法对不同生态环境下(2007-北京、2008-北京、2007-河南、2008-河南、2007-新疆以及2008-新疆)的玉米雄穗分枝数和雄穗重进行QTL定位。同时, 利用基于混合线性模型的QTLNetwork-2.0软件进行基因×环境互作及上位性分析。6个环境下2个群体共检测到51个与雄穗分枝数和雄穗重相关的QTL(Q/H群体32个, Y/H群体19个), 其中包括7个主效QTL, 并在Q/H群体中确定了2个重要的QTL, 即位于7.01bin的Qqtpbn7-1和位于7.02bin的Qqtw7-2。对比2个群体的定位结果, 共挖掘到3个在不同遗传背景下的“一致性”QTL, 这些在不同环境及不同遗传背景下能够稳定存在的QTL可为玉米雄穗相关性状的生产应用以及精细定位提供有价值的参考。     

控制玉米雄穗分枝数目和雄穗重的主效QTL的定位

利用2套具有共同亲本黄早四且分别含有230个及235个家系的F2：3群体,结合2年多点的表型鉴定,运用完备复合区间作图方法对不同生态环境下（2007-北京、2008-北京、2007-河南、2008-河南、2007-新疆以及2008-新疆）的玉米雄穗分枝数和雄穗重进行QTL定位。同时,利用基于混合线性模型的QTLNetwork-2.0软件进行基因×环境互作及上位性分析。6个环境下2个群体共检测到51个与雄穗分枝数和雄穗重相关的QTL（Q/H群体32个,Y/H群体19个）,其中包括7个主效QTL,并在Q/H群体中确定了2个重要的QTL,即位于7.01bin的Qqtpbn7-1和位于7.02bin的Qqtw7-2。对比2个群体的定位结果,共挖掘到3个在不同遗传背景下的＂一致性＂QTL,这些在不同环境及不同遗传背景下能够稳定存在的QTL可为玉米雄穗相关性状的生产应用以及精细定位提供有价值的参考。     

Quantitative trait loci for flowering time and inflorescence architecture in rose

The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F ₁ diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose.     

Inheritance of inflorescence architecture in sorghum

The grass inflorescence is the primary food source for humanity, and has been repeatedly shaped by human selection during the domestication of different cereal crops. Of all major cultivated cereals, sorghum [Sorghum bicolor (L.) Moench] shows the most striking variation in inflorescence architecture traits such as branch number and branch length, but the genetic basis of this variation is little understood. To study the inheritance of inflorescence architecture in sorghum, 119 recombinant inbred lines from an elite by exotic cross were grown in three environments and measured for 15 traits, including primary, secondary, and tertiary inflorescence branching. Eight characterized genes that are known to control inflorescence architecture in maize (Zea mays L.) and other grasses were mapped in sorghum. Two of these candidate genes, Dw3 and the sorghum ortholog of ramosa2, co-localized precisely with QTL of large effect for relevant traits. These results demonstrate the feasibility of using genomic and mutant resources from maize and rice (Oryza sativa L.) to investigate the inheritance of complex traits in related cereals.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Detection and integration of quantitative trait loci for grain yield components and oil content in two connected recombinant inbred line populations of high-oil maize

Improvement in grain yield is an important objective in high-oil maize breeding. In this study, one high-oil maize inbred was crossed with two normal maize inbreds to produce two connected recombinant inbred line (RIL) populations with 282 and 263 F_7:8 families, respectively. The field experiments were conducted under four environments, and eight grain yield components and grain oil content were evaluated. Two genetic linkage maps were constructed using 216 and 208 polymorphic SSR markers. Quantitative trait loci (QTL) were detected for all traits under each environment and in combined analysis. Meta-analysis was used to integrate genetic maps and detected QTL in both populations. A total of 199 QTL were detected, 122 in population 1 and 87 in population 2. Seven, 11 and 19 QTL showed consistency across five environments, across two RIL populations and with respective F_2:3 generations, respectively. 183 QTL were integrated in 28 meta-QTL (mQTL). QTL with contributions over 15% were consistently detected in 3–4 cases and integrated in mQTL. Each mQTL included 3–19 QTL related to 1–4 traits, reflecting remarkable QTL co-location for grain yield components and oil content. Further research and marker-assisted selection (MAS) should be concentrated on 37 consistent QTL and four genetic regions of mQTL with more than 10 QTL at bins 3.04–3.05, 7.02, 8.04–8.05 and 9.04–9.05. Near-isogenic lines for 100-grain-weight QTL at bin 7.02–7.03, for ear-length QTL at bin 7.02–7.03 and for rows-per-ear QTL at bin 3.08 are now in construction using MAS. Co-located candidate genes could facilitate the identification of candidate genes for grain yield in maize.     

Quantitative trait loci controlling plant architectural traits in cotton

Cotton plant architecture is an important characteristic influencing the suitability of specific cotton varieties in cultivation, fiber yield and quality. However, complex multigenic relationships and substantial genotype–environment interaction underlie plant architecture, and will hinder the efficient improvement of these traits in conventional cotton breeding programs. An enhanced understanding of the molecular-genetic regulation of plant morphological developmental can aid in the modification of agronomically relevant traits. In this study, an interspecific Gossypium hirsutum and Gossypium barbadense BC₁ population was used to identify QTL associated with plant architectural traits. Twenty-six single QTL were identified for seven plant architecture traits. The phenotypic variation explained by an individual QTL ranged from 9.56% to 44.57%. In addition, 11 epistatic QTL for fruit branch angle (FBA), plant height (PH), main-stem leaf size (MLS), and fruiting branch internode length (FBI) explained 2.28–15.34% of the phenotypic variation in these traits. The majority of the interactions (60%) occurred between markers linked to QTL influencing the same traits. The QTL detected in this study are expected to be valuable in future breeding programs to develop cultivars exhibiting desirable cotton architecture.     

Joint‐linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize

Both insufficient and excessive male inflorescence size leads to a reduction in maize yield. Knowledge of the genetic architecture of male inflorescence is essential to achieve the optimum inflorescence size for maize breeding. In this study, we used approximately eight thousand inbreds, including both linkage populations and association populations, to dissect the genetic architecture of male inflorescence. The linkage populations include 25 families developed in the U.S. and 11 families developed in China. Each family contains approximately 200 recombinant inbred lines (RILs). The association populations include approximately 1000 diverse lines from the U.S. and China. All inbreds were genotyped by either sequencing or microarray. Inflorescence size was measured as the tassel primary branch number (TBN) and tassel length (TL). A total of 125 quantitative trait loci (QTLs) were identified (63 for TBN, 62 for TL) through linkage analyses. In addition, 965 quantitative trait nucleotides (QTNs) were identified through genomewide study (GWAS) at a bootstrap posterior probability (BPP) above a 5% threshold. These QTLs/QTNs include 24 known genes that were cloned using mutants, for example Ramosa3 (ra3), Thick tassel dwarf1 (td1), tasselseed2 (ts2), liguleless2 (lg2), ramosa1 (ra1), barren stalk1 (ba1), branch silkless1 (bd1) and tasselseed6 (ts6). The newly identified genes encode a zinc transporter (e.g. GRMZM5G838098 and GRMZM2G047762), the adapt in terminal region protein (e.g. GRMZM5G885628), O‐methyl‐transferase (e.g. GRMZM2G147491), helix‐loop‐helix (HLH) DNA‐binding proteins (e.g. GRMZM2G414252 and GRMZM2G042895) and an SBP‐box protein (e.g. GRMZM2G058588). These results provide extensive genetic information to dissect the genetic architecture of inflorescence size for the improvement of maize yield.     

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population

Background

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations.

Results

A set of 708 F₂ progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method.

Conclusions

We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-433) contains supplementary material, which is available to authorized users.     

Mapping QTLs contributing to <Emphasis Type="Italic">Ustilago maydis</Emphasis> resistance in specific plant tissues of maize

Quantitative trait loci (QTL) contributing to the frequency and severity of Ustilago maydis infection in the leaf, ear, stalk, and tassel of maize plants were mapped using an A188 × CMV3 and W23 × CMV3 recombinant inbred (RI) populations. QTLs mapped to genetic bins 2.04 and 9.04–9.05 of the maize genome contributed strongly (R ² = 18–28%) to variation in the frequency and severity of U. maydis infection over the entire plant in both populations and within the majority of environments. QTLs mapped to bins 3.05, 3.08, and 8.00 in the A188 × CMV3 population and bin 4.05 in both populations significantly contributed to the frequency or severity of infection in only the tassel tissue. QTLs mapped to bin 1.07 in the A188 × CMV3 population and bin 7.00 in the W23 × CMV3 population contributed to U. maydis resistance in only the ear tissue. Interestingly, the CMV3 allele of the QTL mapped to bin 1.10 in the A188 × CMV3 population significantly contributed to U. maydis susceptibility in the ear and stalk but significantly increased resistance in the tassel tissue. Digenic epistatic interactions between the QTL mapped to bin 5.08 and four distinct QTLs significantly contributed to the frequency and severity of infection over the entire plant and within the tassel tissue of the A188 × CMV3 population. Several QTLs detected in this study mapped to regions of the maize genome containing previously mapped U. maydis resistance QTLs and genes involved in plant disease resistance. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes

Wild species can be used to improve various agronomic traits in cultivars; however, a limited understanding of the genetic basis underlying the morphological differences between wild and cultivated species hinders the integration of beneficial traits from wild species. In the present study, we generated and sequenced recombinant inbred lines (RILs, 201 F₁₀ lines) derived from a cross between Solanum pimpinellifolium and Solanum lycopersicum tomatoes. Based on a high‐resolution recombination bin map to uncover major loci determining the phenotypic variance between wild and cultivated tomatoes, 104 significantly associated loci were identified for 18 agronomic traits. On average, these loci explained ~39% of the phenotypic variance of the RILs. We further generated near‐isogenic lines (NILs) for four identified loci, and the lines exhibited significant differences for the associated traits. We found that two loci could improve the flower number and inflorescence architecture in the cultivar following introgression of the wild‐species alleles. These findings allowed us to construct a trait–locus network to help explain the correlations among different traits based on the pleiotropic or linked loci. Our results provide insights into the morphological changes between wild and cultivated tomatoes, and will help to identify key genes governing important agronomic traits for the molecular selection of elite tomato varieties.     

Quantitative trait loci for inflorescence development in Arabidopsis thaliana

Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler x Col and Cvi x Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi x Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.     

Detection of QTL for six yield-related traits in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis>) using DH and immortalized F<Subscript>2</Subscript> populations

The inheritance of yield-related traits in rapeseed (Brassica napus) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for such traits are only few. QTL related to six traits were mapped which include plant height (PH), height of lowest primary effective branch (HPB), length of main inflorescence (LMI), silique length (SL), number of primary branches (FB) and silique density (SD). A set of 258 doubled haploid (DH) lines derivatives of a cross between a canola variety Quantum and a resynthesized B. napus line No.2127-17, and a fixed immortalized F₂ (designated as IF₂) population generated by randomly permutated intermating of these DHs were investigated. A genetic linkage map was constructed using 208 SSR and 189 SRAP markers for the DH population. Phenotypic data were collected from three environments for the two populations. Using composite interval mapping analyses, 30 and 22 significant QTL were repeatedly detected across environments for the six traits in the DH and IF₂ populations, respectively. Twenty-nine QTL were common between the two populations. The directions of parental contribution for all common QTL were the same, showing a great potential for marker-assisted selection in improving these traits. Some chromosomal regions harbor QTL for multiple traits, which were consistent with significant phenotypic correlations observed among traits. The results provided a better understanding of the genetic factors controlling yield-related traits in rapeseed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of quantitative trait loci controlling developmental characteristics of Brassica oleracea L

A segregating population of F₁-derived doubled haploid (DH) lines of Brassica oleracea was used to detect and locate QTLs controlling 27 morphological and developmental traits, including leaf, flowering, axillary bud and stem characters. The population resulted from a cross between two very different B. oleracea crop types, an annual cauliflower and a biennial Brussels sprout. A principal component analysis (PCA), based on line means, allowed all the traits to be grouped into distinct categories according to the first five Principal Components. These were: leaf traits (PC1), flowering traits (PC2), axillary bud traits (PC3 and 5) and stem traits (PC4). Between zero and four putative QTL were located per trait, which individually explained between 6% and 43% of the additive genetic variation, using the multiple-marker regression approach to QTL mapping. For lamina width, bare petiole length and stem length two QTL with opposite effects were detected on the same linkage groups. Intra- and inter-specific comparative mapping using RFLP markers identified a QTL on linkage group O8 accounting for variation in vernalisation, which is probably synonymous with a QTL detected on linkage group N19 of Brassica napus. In addition, a QTL for petiole length detected on O3 of this study appeared to be homologous to a QTL detected on another B. oleracea genetic map (Camargo et al. 1995). Received: 28 March 2001 / Accepted: 25 June 2001     

Morphological traits defining species differences in wild relatives of maize are controlled by multiple quantitative trait loci

We analyzed the genetic basis of morphological differences between two wild species of teosinte (Zea diploperennis and Z. mays ssp. parviglumis), which are relatives of maize. These two species differ in a number of taxonomically important traits including the structure of the tassel (male inflorescence), which is the focus of this report. To investigate the genetic inheritance of six tassel traits, quantitative trait locus (QTL) mapping with 95 RFLP markers was employed on a population of 425 F2 plants. Each trait was analyzed by interval mapping (IM) and composite interval mapping (CIM) to identify and characterize the QTL controlling the differences in tassel morphology. We detected two to eight QTL for each trait. In total, 30 QTL with IM and 33 QTL with CIM were found for tassel morphology. QTL for several of the traits mapped near each other, suggesting pleiotropy and/or linkage of QTL. The QTL showed small to moderate magnitudes of effect. No QTL of exceptionally large effect were found as seen under domestication and in the case of some other natural species. Thus, the model involving major QTL of large effect seems not to apply to the traits and species analyzed. A mixture of QTL with positive and negative allelic effects was found for most tassel traits and may suggest a history of periodic changes in the direction of selection during the divergence of Z. diploperennis and Z. mays ssp. parviglumis or fixation of QTL alleles by random genetic drift rather than selection.     

QTLs of cold tolerance-related traits at the booting stage for NIL-RILs in rice revealed by SSR

QTLs for cold tolerance-related traits at the booting stage using balanced population for 1525 recombinant inbred lines of near-isogenic lines (viz.NIL-RILs for BC5F3 and BC₅F₄ and BC₅F₅) over 3 years and two locations by backcrossing the strongly cold-tolerant landrace (Kunmingxiaobaigu) and a cold-sensitive cultivar (Towada) was analyzed. In this study, 676 microsatellite markers were employed to identify QTLs conferring cold tolerance at booting stage. Single marker analysis revealed that 12 markers associated with cold tolerance on chromosome 1, 4 and 5. Using a LOD significance threshold of 3.0,compositive interval mapping based on a mixed linear model revealed eight QTLs for 10 cold tolerance-related traits on chromosomes 1, 4, and 5. They were tentatively designatedqCTB-1-1, qCTB-4-1, qCTB-4-2, qCTB-4-3, qCTB-4-4, qCTB-4-5, qCTB-4-6, andqCTB-5-1. The marker intervals of them were narrowed to 0.3-6.8 cM. Genetic distances between the peaks of the QTL and nearest markers varied from 0 to 0.04 cM. We were noticed in some traits associated cold tolerance, such asqCTB-1-1 for 5 traits (plant height, panicle exsertion, spike length, blighted grains per spike and spikelet fertility),qCTB-4-1 for 8 traits (plant height, node length under spike, leaf length, leaf width, spike length, full grains per spike, total grains per spike and spikelet fertility),qCTB-4-2 for 3 traits (spike length, full grains per spike and spikelet fertility),qCTB-5-1 for 5 traits (plant height, panicle exsertion, blighted grains per spike, full grains per spike and spikelet fertility). The variance explained by a single QTL ranged from 0.80 to 16.80%. Three QTLs (qCTB-1-1, qCTB-4-1, qCTB-4-2) were detected in two or more trials. Our study sets a foundation for cloning cold-tolerance genes and provides opportunities to understand the mechanism of cold tolerance at the booting stage.     

INFLORESCENCE DEVELOPMENT IN TWO ANNUAL TEOSINTES: ZEA MAYS SUBSP. MEXICANA AND Z. MAYS SUBSP. PARVIGLUMIS

The ontogeny of tassels and ears in two annual Mexican teosintes, Zea mays subsp. mexicana and Z. mays subsp. parviglumis, was examined using scanning electron microscopy and light microscopy. Ear development in these annual teosintes follows a pattern previously described as leading to the bisexual mixed inflorescence in Z. diploperennis. Common bud primordia are initiated in the axils of distichously arranged bracts along the ear axis. These common primordia bifurcate to form paired sessile and pedicellate spikelet primordia. Development of pedicellate spikelets is arrested leaving the sessile spikelets, along with the adjoining rachis segment, to form solitary grains enclosed within cupulate fruitcases. Development of the central tassel spike is similar to that previously described in the Z. diploperennis tassel, except that the first formed axillary bud primordia form precocious tassel branches. The origin of these tassel branches suggests a possible mechanism for the transition from a distichous spike, characteristic of teosinte, to a polystichous spike, typical of maize.