Genetic detection of node of first fruiting branch in crosses of a cultivar with two exotic accessions of upland cotton

Flowering time has biological and agricultural significance for crops. In Upland cotton (Gossypium hirsutum L.), photoperiodic sensitivity is a major obstacle in the utilization of primitive accessions in breeding programs. Quantitative trait loci (QTLs) analysis was conducted in two F₂ populations from the crosses between a day-neutral cultivar Deltapine 61 (DPL61) and two photoperiod sensitive G. hirsutum accessions (T1107 and T1354). Node of first fruiting branch (NFB) was used to measure relative time of flowering. Different flowering time genetic patterns were observed in the two populations. Two QTLs were found across five scoring dates, accounting 28.5 (qNFB-c21-1) and 15.9% (qNFB-c25-1) of the phenotypic variation at the last scoring date in Pop. 1107 (DPL61 by T1107); whereas, one major QTL (qNFB-c25-1) can be detected across five scoring dates, explained 63.5% of the phenotypic variation at the last scoring date in Pop. 1354 (DPL61 by T1354). QTLs with minor effects appeared at various scoring date(s), indicating their roles in regulating flowering at a lower or higher node number. Genetic segregation analysis and QTL mapping results provide further information on the mechanisms of cotton photoperiodic sensitivity. Part of a Ph.D. dissertation by senior author submitted to the Department of Plant and Soil Sciences, Mississippi State University, December 2007. Contribution of USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn. Journal paper J. 11276 of Mississippi Agric. and Forestry Exp. Stn.     

Genetic diversity for agronomic and fiber traits in day-neutral accessions derived from primitive cotton germplasm

Upland cotton (Gossypium hirsutumL) is an important crop that is cultivated in warm climates through-out the world. Agronomic performance and fiber quality must continually be improved if cotton is to maintain economic viability. Primitive ancestors of cotton contain diversity for trait improvement; however, many of these accessions have a short-day flowering response (photoperiodic) and are not readily useable in breeding programs. In this study, 114 day-neutral derived primitive germplasm lines were evaluated in field trials for two years. Agronomic and fiber trait data were collected and analyzed. Variance components, genotypic values, and genotypic correlations were calculated. Genotypic effects for all traits studied made significant contributions to the phenotypic variation indicating genetic diversity among these lines. The predicted genotypic values showed a wide range of variation for agronomic and fiber traits. Weak genotypic correlations were found between yield and 2.5% span length and fiber strength, two important fiber traits. Although these day-neutral derived accessions had lower lint percentage, they had improved fiber length, strength, micronaire, and comparable yields with two commercial cultivars. Thus, these day-neutral derived accessions are sources of genetic variation that when used in breeding programs offer the potential to improve important traits and expand genetic diversity.Contribution of the USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

Quantitative trait analysis of flowering time in spring rapeseed (B. napus L.)

The inheritance of flowering time trait in spring-type rapeseed (Brassica napus L.) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for the trait are only few. We identified QTL underlying variation for flowering time in a doubled haploid (DH) mapping population of nonvernalization-responsive canola (B. napus L.) cultivar 465 and line 86 containing introgressions from Houyou11, a Chinese early-flowering cultivar in Brassica rapa L. Significant genetic variation in flowering time and response to photoperiod were observed among the DH lines from 465/86. A molecular linkage map was generated comprising three types of markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 4 major loci, localized on four different linkage groups A6, A7, C8 and C9. These loci each accounted for between 9.2 and 12.56 % of the total genotypic variation for first flowering. The published high-density maps for flowering time mapping used different marker systems, and the parents of our crosses have different genetic origins, with either spring-type B. napus or B. rapa. So we cannot determine whether the QTL on the same linkage groups were in the same region or not. There was evidence of additive × additive epistatic effects for flowering time in the DH population. Epistasis existed not only between main-effect QTLs, but also between QTLs with minor effects. Four pair of epistasis effects between minor QTLs explained about 20 % of the genetic variance observed in the DH population. The results indicated that minor QTLs for flowering time should not be ignored. Significant genotypes × environment interactions were also found for the quantitative traits, and with significant change in the ranking of the DH lines in different environments. The results implied that FQ3 was a non-environment-specific QTL and may control flowering time by autonomous pathway. FQ4 were winter-environment-specific QTL and may control flowering time by photoperiod-pathway. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for high altitude areas, via marker-assisted selection.     

Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton

Genetic mapping is an essential tool for cotton (Gossypium hirsutum L.) molecular breeding and application of DNA markers for cotton improvement. In this present study, we evaluated an RI population including 188 RI lines developed from 94 F₂-derived families and their two parental lines, ‘HS 46’ and ‘MARCABUCAG8US-1-88’, at Mississippi State, MS, for two years. Fourteen agronomic and fiber traits were measured. One hundred forty one (141) polymorphic SSR markers were screened for this population and 125 markers were used to construct a linkage map. Twenty six linkage groups were constructed, covering 125 SSR loci and 965 cM of overall map distance. Twenty four linkage groups (115 SSR loci) were assigned to specific chromosomes. Quantitative genetic analysis showed that the genotypic effects accounted for more than 20% of the phenotypic variation for all traits except fiber perimeter (18%). Fifty six QTLs (LOD > 3.0) associated with 14 agronomic and fiber traits were located on 17 chromosomes. One QTL associated with fiber elongation was located on linkage group LGU01. Nine chromosomes in sub-A genome harbored 27 QTLs with 10 associated with agronomic traits and 17 with fiber traits. Eight chromosomes in D sub-genome harbored 29 QTLs with 13 associated with agronomic traits and 16 with fiber traits. Chromosomes 3, 5, 12, 13, 14, 16, 20, and 26 harbor important QTLs for both yield and fiber quality compared to other chromosomes. Since this RI population was developed from an intraspecific cross within upland cotton, these QTLs should be useful for marker assisted selection for improving breeding efficiency in cotton line development. Paper number J1116 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

陆地棉重组近交系产量及其构成因素的QTL分析

利用爱字棉1517×德州047重组近交系(recombinant inbred lines, RIL)中G6群体构建的SSR遗传连锁图谱及基于混合线性模型的复合区间作图法对QTL进行定位,并对主效QTL,加性×加性上位性QTL及与环境互作效应进行分析,为利用分子聚合方法提高产量提供理论依据。对2006年、2008年以及2009年的产量性状进行分离分析,检测到24个不同年份的主效QTL,其中相关于单株籽棉、单株皮棉、衣分、子指以及单株铃数的分别检测到1个不同年份稳定存在的主效QTL;对3年的产量性状作环境因子联合分析,检测到14个主效QTL,其中6个与环境互作,检测到20对加加上位性QTL,其中7对与环境互作。不同年份检测的稳定且受环境影响小或不受环境影响的与近处标记紧密连锁的主效QTL可用于分子标记辅助选择,以提高育种的效率。     

Identification of QTLs for phenolic compounds in oilseed rape (<Emphasis Type="Italic">Brassica napus L.</Emphasis>) by association mapping using SSR markers

Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. In this study, association mapping was performed to detect QTL-linked and genome wide SSR markers linked to phenolic compounds of extraction meal in a population of 49 genetically diverse oilseed rape cultivars of dark-seeded, winter-type oilseed rape accessions. Correction for population structure was performed using 559 genome wide SSR markers. Results showed that seed colour is an important contributor to seed meal quality. Totally, 52 SSR markers linked to phenolic compounds were detected, five of them being QTL linked markers. Some of these markers were already mapped on Brassica napus chromosomes that contain known QTL controlling oilseed rape meal quality traits. Our results demonstrate that association mapping is a useful approach to complement and enhance previous QTL information for marker-assisted selection.     

多环境下陆地棉(Gossypium hirsutum L.)重组自交系铃重与衣分性状的QTL分析

本研究利用以SGK9708为母本,0-153为父本构建的196个陆地棉重组自交系(F6:8)构建了包含186个标记,总长827.84 cM,标记间平均距离4.45 cM,覆盖棉花基因组18.6%的遗传连锁图谱,并对7个环境下的铃重和衣分性状进行QTL定位和上位性互作分析.利用两种分析软件(WinQTLcart2.5和Q...     

Identification of population-specific QTLs for flowering in soybean

Flowering is an important stage in plant development and crucial for adaptation of plant species to different environments. Two soybean mapping populations were used to identify quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) by genotyping simple sequence repeat (SSR) markers. Single-factor analysis of variance detected association of phenotypic data with SSR markers in each population. DF QTLs were identified on four chromosomes (chrs.); two QTLs located on chrs. 2 and 13 with Satt041 and Satt206 in the Jinpumkong 2 × SS2-2 population and other two DF QTLs were detected on chrs. 6 and 19 with Satt100 and Satt373 in the Iksannamulkong × SS2-2 population. The major QTLs associated with Satt100 explained 30.3% of maximum phenotypic variation. Especially, all DF QTLs included QTLs for DM, except Satt206 on chr. 13. Moreover, two additional DM QTLs were mapped on chrs. 10 and 11 with Satt243 and Satt359, respectively. DF QTL on chr. 2 with Satt041 was the newly identified QTL only in the Jinpumkong 2 × SS2-2 population and explained 10.3% of the phenotypic variation. The single locus of Satt100 on chr. 6 and Satt373 on chr. 19 were located on soybean genomic regions of the known flowering gene loci E1 and E3, respectively. These population-specific QTLs (Satt100 and Satt373) are the major QTLs for flowering time, putatively, they may be related to maturity QTLs with large effect. Additionally, these QTLs are valuable for marker-assisted approaches and could be widely adopted by soybean breeders.     

Genetic association of cotton yield with its component traits in derived primitive accessions crossed by elite upland cultivars using the conditional ADAA genetic model

Boll number, lint percentage, and boll weight are three component traits for lint yield of upland cotton, Gossypium hirsutum L. Selecting high yielding lines or hybrids depends on the ability to dissect the genetic relationship of lint yield with these component traits. In this study, 14 day-neutral lines with desirable fiber quality derived from primitive accessions were top crossed with five commercial cultivars. The F₂ populations and parents were grown in one location in 1998 and two locations in 1999 at Mississippi State, MS. The F₃ populations and parents were grown in two locations in 2000. Lint yield and three component traits were measured and analyzed by the ADAA genetic model with the mixed model based conditional approach. Results showed that boll number or boll number with lint percentage or boll weight contributed to the majority of the phenotypic variance and variance components for lint yield. Boll number was more important than the other two component traits in terms of various genetic effects. The results also showed that the combination of boll number and boll weight greatly increased the contribution to lint yield even though boll weight itself had no significant contribution to lint yield compared to boll number alone. The genetic contribution effects were also predicted due to single component traits or their combinations for parents and crosses. The results revealed that the balanced selection of boll weight and boll number should be considered to obtain high yielding hybrids or pure lines. Contribution of the USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

Molecular mapping of major genes and quantitative trait loci determining flowering time in response to photoperiod in barley

Two major genes (eam8 and eam10) and two quantitative trait loci (QTL) determining flowering time in barley were associated with restriction fragment length polymorphism markers. The loci eam8 and eam10 were found to map in regions of chromosomes 1HL and 3HL, respectively, already estimated from previous classical linkage analyses. While investigating doubled haploid lines of a spring habit barley mapping population, two QTL for flowering time were detected on chromosomes 1HL and 7HS, respectively, when the material was grown under long photoperiod conditions. When growing the same lines under short photoperiod, no QTL were discernible. Allelic and homoeologous relationships with flowering time loci described earlier in barley and other Triticeae species are discussed.     

陆地棉光合相关性状的QTL定位分析

光合作用是棉花产量的主要物质来源。本研究以高光效陆地棉冀优861和低光效陆地棉新陆早25号为亲本组配的196个F₂单株为作图群体,利用SSR（Simple Sequence Repeat）标记构建陆陆杂交遗传连锁图谱,共有30个标记位点连锁,包含4个连锁群,全长244.4cM。利用QTL IciMapping 4.1软件的完备区间作图法对冀优861×新陆早25号F_2:3家系的光合相关性状进行QTL作图分析,共定位到光合相关5个性状的10个QTLs,其中1个光合速率QTL和1个胞间CO₂浓度QTL分别定位在D3和D7染色体上。本研究为棉花光合相关性状QTL的精细定位及分离克隆打下基础,为聚合棉花高光效分子标记辅助育种提供理论依据。     

Fine mapping of a major flowering time QTL on soybean chromosome 6 combining linkage and association analysis

Flowering time is a key trait in the plant life cycle and an important selection criterion for soybean. Here, we combine the advantages of genome-wide association and linkage mapping to identify and fine map quantitative trait loci (QTLs) associated with flowering time. Linkage mapping was performed using 152 recombinant inbred lines and a major QTL, qFT6, affecting flowering time was found on chromosome 6. To refine the qFT6, the 192 natural accessions were genotyped using eight new simple sequence repeats and 10 single nucleotide polymorphisms markers covering the qFT6 region Haplotype analysis showed that the haplotype between markers BARC-014947-01929 and Satt365 could explain more phenotypic variation (26.5 %) than any other combination of markers. These results suggested that the target flowering time gene was located in ~300 kb between BARC-014947-01929 and Satt365, including three predicted genes. High-resolution map in qFT6 region will be useful not only for marker-assisted selection of flowering time but also for further positional cloning of the target gene. These results indicate that combining association and linkage mapping provides an efficient approach for fine mapping of soybean genes.     

Identification of quantitative trait loci across interspecific F2, F2:3 and testcross populations for agronomic and fiber traits in tetraploid cotton

The most widely grown tetraploid Gossypium hirsutum and G. barbadense differ greatly in yield potential and fiber quality and numerous quantitative trait loci (QTLs) have been reported. However, correspondence of QTLs between experiments and populations is poor due to limited number of markers, small population size and inaccurate phenotyping. The purpose of the present study was to map QTLs for yield, yield components and fiber quality traits using testcross progenies between a large interspecific F₂ population and a commercial cotton cultivar as the tester. The results were compared to these from its F₂ and F_2:3 progenies. Of the 177 QTLs identified from the three populations, 65 fiber QTLs and 51 yield QTLs were unique with an average of 8–12 QTLs per traits. All the 26 chromosomes carried QTLs, but differed in the number of QTLs and the number of QTLs between fiber and yield QTLs. The congruence of QTLs identified across populations was higher (20–60 %) for traits with higher heritabilities including fiber quality, seed index and lint percentage, but lower (10–25 %) for lower heritability traits-seedcotton and lint yields. Major QTLs, QTL clusters for the same traits and QTL ‘hotspots’ for different traits were also identified. This research represents the first report using a testcross population in QTL mapping in interspecific cotton crosses and provides useful information for further comparative analysis and marker-assisted selection.     

QTL detection for flowering time in faba bean and the responses to ambient temperature and photoperiod

Faba bean (Vicia faba L.) is a grain legume primarily used for animal feed and human food grown in a range of environments, globally. Time of flowering in faba bean is critical for adaptation to specific environments and is controlled largely by factors such as ambient temperature and photoperiod. The aim of this study was to investigate the genetic control of flowering time and the responses of flowering time to ambient temperature and photoperiod in faba bean. A bi-parental recombinant inbred line population (Icarus × Ascot) was evaluated over three years in field trials and three different controlled environments with varying temperatures and photoperiods. QTL analysis identified eight regions of co-localised QTLs associated with days to flowering, thermal time to flowering and node of first flower; on Chr-I.A/III/V, Chr-I.B.3, Chr-III.1, Chr-III.2, Chr-V.1 and Chr-V.2. Two of the detected regions are common with previously detected QTLs, up to two more are possibly common and the remaining four appear to be novel. For the first time, the associations of these QTLs with ambient temperature and photoperiod response were described. Candidate genes for some of the QTLs were identified using the associations with ambient temperature and photoperiod response together with knowledge extended from other legumes that have a syntenic relationship with faba bean.     

RFLP mapping of QTLs for photoperiod response in tropical sorghum

Genetic control of flowering time in sorghum was investigated using a recombinant inbred lines population derived from a cross between IS 2807, a slightly photoperiod sensitive tropical caudatum landrace, and IS 7680,a highly photoperiod sensitive tropical guinea landrace. Progenies were sown with their parents at six different dates between 1995 and 1997 in Burkina Faso. Direct field measures and synthetic measures derived from the implementation of a model were used to characterize the photoperiod response. Emphasis was put to identify the most relevant traits to account for Basic Vegetative Phase (BVP) and photoperiod sensitivity sensus stricto. One QTL was detected on Linkage Group (LG) F for the traits related to BVP. Two QTLs were detected on LGs C and H for the traits related to the photoperiod sensitivity sensus stricto. This gives credit to at least partially independent genetic determinisms for those two components of photoperiod response. Evidences for possible orthology of the QTLs detected here with other QTLs and major genes involved in flowering time of sorghum and rice are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Quantitative Traits Locus Meta-analysis of Fiber Quality Traits in Cotton

Using bioinformatics methods and meta-analysis with BC₁ map as reference, 92 cotton fiber quality QTL collected from both BC₁ and BC₁F₂ populations constructed previously were used to construct a QTL integrated map for QTL analysis in this study. The five hundred ninety-nine loci were mapped into 26 chromosomes with an average distance between adjacent markers of 5.96 cM and covered 3,571.9 cM. Sixty-three QTL of fiber qualities related were integrated into the new reference map. The fifteen meta-QTL were mapped on 12 chromosomes by the meta-analysis method and also QTL clusters have been discovered on chromosome 9, 16 and 24. The major meta-QTL of Meta-QTL9-1 derived from five QTL on chromosome 9, could explain 17.16% of phenotypic variance. The meta-QTL16-1 derived from ten QTL on chromosome 16, could explain 12.28% of phenotypic variance. And three meta-QTL derived from nine QTLs on chromosome 24, could explain 16.12%,16.69% and 18.27% of phenotypic variance, respectively. On average, one meta-QTL derived from two QTLs on the other chromosomes. The results indicated that these meta-QTL could be used in improving fine QTL mapping and molecular-assisted selection of cotton fiber qualities in breeding.     

高产棉花品种泗棉3号产量及其构成因素的QTL标记和定位

利用我国长江流域大面积种植的高衣分、高产品种泗棉3号和西班牙陆地棉栽培品种Carmen,构建RIL作图群体,在3个环境中进行产量及其构成因素的QTLs标记和定位,研究了泗棉3号高产特性的分子机理。用2 523对SSR引物,进行双亲的多态性检测,其中62对（2.46%）有多态性,它们共产生65个稳定的多态性位点。通过复合区间作图,共检测到1个单株果节数、1个铃重、2个籽指、1个衣指和1个百粒籽棉重等8个产量构成因素的QTLs。单标记分析还在多环境中检测到17个产量构成因素的QTLs。与这些QTLs紧密连锁的分子标记可以用于对产量及其构成因素的分子标记辅助选择。     

多环境下水稻DH群体剑叶长度的QTL分析

种植由籼稻品种和粳稻品种杂交衍生的DH群体,连续4年测定剑叶长度,运用基于混合模型的复合区间作图法,定位其QTL及上位性互作,估算遗传主效应和环境互作效应。结果表明,全部18个QTL都参与了上位性的形成,其中3个没有自身的遗传效应,但参与了3对上位性互作,这是传统方法不能发现的。另外,一个QTL可与多个QTL发生互作,这可能预示着存在更高阶互作。QTL与上位性互作可以具有不受环境影响而稳定表达的效应,以及与环境的互作效应。有些QTL与环境的互作效应可以在多环境下被检测到,但却不具有主效应,这种QTL可能易受环境因子的影响。QTL与环境的互作效应为随机效应,一个QTL或一对上位性与环境的互作效应总和理论上应等于零,否则会影响对遗传效应的估算,因此多环境下估算的遗传效应更可靠。     

Identification of quantitative trait loci for flowering-related traits in the D genome of synthetic hexaploid wheat lines

The gene pool of Aegilops tauschii, the D-genome donor of common wheat (Triticum aestivum L.), can be easily accessed in wheat breeding, but remains largely unexplored. In our previous studies, many synthetic hexaploid wheat lines were produced through interspecific crosses between the tetraploid wheat cultivar Langdon and various A. tauschii accessions. The synthetic hexaploid wheat lines showed wide variation in many characteristics. To elucidate the genetic basis of variation in flowering-related traits, we analyzed quantitative trait loci (QTL) affecting time to heading, flowering and maturity, and the grain-filling period using four different F₂ populations of synthetic hexaploid wheat lines. In total, 10 QTLs located on six D-genome chromosomes (all except 4D) were detected for the analyzed traits. The QTL on 1DL controlling heading time appeared to correspond to a flowering time QTL, previously considered to be an ortholog of Eps-A ^m 1 which is related to the narrow-sense earliness in einkorn wheat. The 5D QTL for heading time might be a novel locus associated with wheat flowering, while the 2DS QTL appears to be an allelic variant of the photoperiod response locus Ppd-D1. Some of the identified QTLs seemed to be novel loci regulating wheat flowering and maturation, including a QTL controlling the grain filling period on chromosome 3D. The exercise demonstrates that synthetic wheat lines can be useful for the identification of new, agriculturally important loci that can be transferred to, and used for the modification of flowering and grain maturation in hexaploid wheat.     

Evaluation of genetic variances, heritabilities, and correlations for yield and fiber traits among cotton F2 hybrid populations

Summary F₂ hybrid cultivars continue to occupy a small portion of the cotton (Gossypium hirsutum L.) production are in the United States, but occupy a larger proportion of the production area in some other countries. Sixty-four F₂ hybrids resulting from crosses of four commercial cultivars and 16 pest-resistant germplasm lines were evaluated for five fiber and four yield traits in four environments at Mississippi State, MS. An additive-dominance genetic model was employed for these traits. The minimum norm quadratic unbiased estimation (MINQUE) method was used with a mixed model approach for estimating genetic variance and covariance components and for predicting genetic correlations. This study investigated genetic variances, heritabilities, and genetic and phenotypic correlations between agronomic and fiber traits among these 64 F₂ hybrid populations and discussed the usefulness of these populations for use as hybrids or for selections for pure lines.Dominance variance accounted for the major proportion of the phenotypic variances for lint yield, lint percentage, and boll size indicating that hybrids should have an advantage for these traits compared to pure lines. A low proportion of additive variance for fiber traits and the significant additive x environment variance components indicated a lack of substantial useful additive genetic variability for fiber traits. This suggests that selections for pure lines within these F₂ populations would have limited success in improving fiber traits. Genetic and phenotypic correlation coefficients were of comparable magnitude for most pairs of characters. Fiber strength showed a positive additive genetic correlation with boll weight. Dominance genetic correlations of fiber strength with elongation and 2.5% span length were also significant and positive; however, the additive genetic correlation of length and strength was zero.Contribution of the USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn.