Chromosomal regions controlling anther culturability in rice (Oryza sativa L.)

Diallel analysis has revealed that anther culturability in rice (Oryza sativa L.) is a quantitative trait controlled by the nuclear genome. Mapping of anther culturability is important to increase the efficiency for green plant regeneration from microspores. In the previous study, we detected distorted segregation of RFLP markers in rice populations derived from the anther culture of an F₁ hybrid between a japonica cultivar ‘Nipponbare’ and an indica cultivar ‘Milyang 23’. To clarify the association between chromosomal regions showing distorted segregation and anther culturability, the anther culturability of doubled haploid lines derived from the same cross combination was examined, and the association between alleles of the RFLP markers, which exhibiting the most distorted segregation on chromosomes 1, 3, 7, 10 and 11, and the anther culturability was evaluated. One region on chromosome 1 was found to control callus formation from microspores, and one region on chromosome 10 appeared to control the ratio of green to albino regenerated plants. In both regions, the Nipponbare allele had positive effects. Three regions on chromosomes 3, 7 and 11, however, showed no significant effect on anther culturability. This revised version was published online in August 2006 with corrections to the Cover Date.     

Detection of quantitative trait loci for leaf rust resistance in wheat––T. timopheevii/T. tauschii introgression lines

Advanced backcross QTL analysis was used to identify QTLs for seedling and adult plant resistance to leaf rust in introgression lines derived from a cross between the spring wheat cultivar ‘Saratovskaya 29’ and a synthetic allopolyploid wheat (T. timopheevii/T. tauschii). F₂ mapping populations involving two backcross selections (‘BC5’ and ‘BC9’ lines) were genotyped with microsatellite markers. Two significant QTL for adult plant resistance were identified in line ‘BC5’: one on chromosome 2B, but originating from chromosome 2G, explained 31% of the trait variance. The other, derived from T. tauschii and mapped to the short arm of chromosome 2D explained 19% of the trait variance. In the second line, one major seedling and adult plant resistance QTL was identified on chromosome 2B. Both QTL co-located to the same marker interval. Such introgression lines, resulting from the reconstruction of common wheat genome, are of interest both as initial material for breeding and improvement of current cultivars, and as a resource for the study of the interaction and transformation of genomes.     

Dissection of genetic variance of fibre quality in advanced generations from an interspecific cross of Gossypium hirsutum and G. barbadense

The interspecific genetic introgression approach has been shown to facilitate the detection and dissection of quantitative trait loci (QTL). A population consisting of 121 F₆ recombinant inbred lines was developed by crossing Gossypium hirsutum cv. ‘Handan 208’ and G. barbadense cv. ‘Pima 90’ via single‐seed descent. Genotyping indicated that the mean ‘Pima 90’ allele frequency at each locus was 21%. Phenotyping and phenotypic distribution indicated a trend of return of individual lines’ characters to ‘Handan 208’ coupled with a wide variance for each trait. Significant loci influencing fibre quality were detected by one‐way analysis of variance (anova; P < 0.005) and association analysis [?log₁₀(P) ≥ 3]: five and three markers for fibre length, four and one marker(s) for uniformity, two and one marker(s) for micronaire, 13 and 15 markers for strength, six and 10 markers for elongation, respectively. Two‐way anova based on genotypes of all marker loci combination showed that 807 two‐locus combinations were significant, and two‐way anova based on marker genotypes of QTL markers combination showed five significant digenic interactions (P < 0.01).     

Phenylacetic acid stimulation of direct shoot formation in anther and somatic tissue cultures of rice (Oryza saliva L.)

The effect of phenylacetic acid (PAA) on rice (Oryza saliva L.) anther culture was investigated with six genotypes, using 2,4-D as control. In the two-step culture protocol, replacing 2, 4-D with PAA in the induction medium did not influence callus induction but significantly improved the shoot differentiation from callus, particularly in the indica cultivar Teqing. The anther-derived calli of all genotypes regenerated shoots directly on the callus induction medium containing PAA. Most of the directly-regenerated plantlets had well-developed root systems and were therefore readily transplanted into soil. The improved shoot differentiation potential and the frequency of direct regeneration depended on genotype, basal medium and PAA concentration. The one-step green shoot regeneration frequencies obtained were 1.98% with the indica cultivar ‘129’, 1.5% with the indica × japonica hybrid ‘Teqing/02428’ (F₁), and 1.98% with the indica × indica hybrid ‘Waiyin 2/C.B.’ (F₁). The PAA-based one-step method was most effective on the anther culture of indica genotypes. Three DH populations have been constructed from hybrids (F₁) via one-step culture. PAA also enhanced the one-step plantlet formation in rice somatic tissue culture.     

杂交粳稻亲本米质性状优异配合力的标记基因型鉴定

杂交粳稻米质整体水平不如常规粳稻也是限制杂交粳稻广泛种植的原因之一。本研究选用115个SSR引物扩增6个粳稻BT型不育系和12个恢复系的标记基因型,并分析72个F₁组合谷粒长、谷粒宽、糙米率、精米率、整精米率、垩白米率、垩白度、糊化温度、胶稠度和直链淀粉含量10个米质性状的配合力,结合亲本SSR分子标记数据和性状配合力数据筛选了10个米质性状优异配合力的标记基因型。结果共鉴定出30个SSR标记基因型与亲本10个米质性状配合力显著相关,其中25个与亲本米质性状不良配合力相关,5个与优异配合力相关。标记基因型RM263-175/180和RM444-230/240可以使F₁整精米率分别提高3.2%和2.5%。RM3-120/150可以使F₁谷粒长缩短2.4%,RM444-180/240可以使F₁谷粒宽增加2.1%。RM428-273/294可以使F₁植株上的杂交稻米直链淀粉含量减少7.0%。有8个标记基因型同时也影响产量性状配合力。RM3-120/150同时可以使F₁的每穗总粒数和每穗实粒数分别增加15.9%和10.9%。RM1211-150/160可使F₁的糙米率和精米率分别减少0.9%和1.1%,同时使F₁的每穗总粒数和每穗实粒数分别增加21.8.%和20.4%。RM23-150/160可使F₁的垩白米粒率和垩白度分别增加44.1%和45.7%,同时使F₁的单株日产量和每穗总粒数分别增加11.2%和11.6%。这些结果可用于指导亲本米质性状和产量性状配合力的分子标记辅助改良以及未来杂交粳稻组合配置中的亲本选配。     

Fine mapping the QTL qFS‐chr.23, using a CSIL

In an earlier advanced‐backcross quantitative trait locus (QTL) analysis of an interspecific cross of Gossypium hirsutum cv. ‘Xinluzhong 36’(‘XLZH36’) and G. barbadense cv. ‘Xinhai 21’(‘XH21’), a QTL for fibre strength in the chromosome segment introgression line IL23‐09 was analysed. Single marker analysis revealed that the markers on chro.23 were associated with fibre strength. Using composite interval mapping with the F₂ population (1296 plants), a QTL for fibre strength was detected on chro. 23. The QTL explained 8.9% and 15.9% of phenotypic variances in the F₂ and F_2 : 3 generations, respectively. Substitution mapping suggested that the QTL was located at a physical distance of 23.4 kb between the markers BNL1414 and the single nucleotide polymorphism (SNP) locus D09_43776813 C‐G. We designated this QTL as qFS‐chr.23 (quantitative trait locus for fibre strength on chro.23). This work provides a valuable genetic resource for the breeding of high fibre quality in cotton and will facilitate future efforts for map‐based cloning.     

Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat

The objectives of this study were to validate the major quantitative trait locus (QTL) for scab resistance on the short arm of chromosome 3B in bread wheat and to isolate near‐isogenic lines for this QTL using marker‐assisted selection (MAS). Two resistant by susceptible populations, both using ‘Ning7840’ as the source of resistance, were developed to examine the effect of the 3BS QTL in different genetic backgrounds. Data for scab resistance and simple sequence repeat (SSR) markers linked to the resistance QTL were analyzed in the F_2:3 lines of one population and in the F_3:4 lines of the other. Markers linked to the major QTL on chromosome 3BS in the original mapping population (‘Ning7840’/‘Clark’) were closely associated with scab resistance in both validation populations. Marker‐assisted selection for the QTL with the SSR markers combined with phenotypic selection was more effective than selection based solely on phenotypic evaluation in early generations. Marker‐assisted selection of the major QTL during the seedling stage plus phenotypic selection after flowering effectively identified scab resistant lines in this experiment. Near‐isogenic lines for this 3BS QTL were isolated from the F₆ generation of the cross ‘Ning7840’/‘IL89‐7978’ based on two flanking SSR markers, Xgwm389 and Xbarc147. Based on these results, MAS for the major scab resistance QTL can improve selection efficiency and may facilitate stacking of scab resistance genes from different sources.     

Anther culture in connection with induced mutations for rice improvement

Doubled haploids have long been recognized as a valuable tool in plant breeding since it not only offers the quickest method of advancing heterozygous breeding lines to homozygosity, but also increases the selection efficiency over conventional procedures due to better discrimination between genotypes within any one generation. Ten cultivars of japonica rice and nine cultivars of indica rice were evaluated for androgenic response. Various doses (10–50 Gy) of gamma rays were applied to investigate the effect of radiation on callus formation, green plant regeneration and the frequency of selected doubled haploid mutants. Similarly, the effects of colchicine concentration (10–200 mg/l) on callus induction, regeneration and fertility of green plants were observed. It was demonstrated that the dose of 20 Gy gamma rays and 30 mg/l concentration of colchicine have significant stimulation effect on regeneration of green plants from rice anther culture. The high frequency of observed doubled haploid mutants indicates that anther culture applied in connection with gamma rays is an effective way to improve rice cultivars. This revised version was published online in August 2006 with corrections to the Cover Date.     

Development of high yielding IR64 × <Emphasis Type="Italic">Oryza rufipogon</Emphasis> (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers’ fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC₂F₆ progenies, selected from among more than 100 BC₂F₅ progenies were evaluated for yield and yield components. For plant height, days to 50% flowering and tillers/plant, the introgression lines did not show any significant change compared to the recurrent parent IR64. For yield, 9 of the 12 introgression lines showed significantly higher yield (19–38%) than the recurrent parent IR64. Four of these lines originating from a common lineage showed higher yield due to increase in grain weight and another three also from a common lineage showed yield increase due to increase in grain number per panicle. For analyzing the introgression at molecular level all the 12 lines were analyzed for 259 polymorphic SSR markers. Of the total 259 SSR markers analyzed, only 18 (7.0%) showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6 and 11. Graphical genotypes have been prepared for each line and association between the introgression regions and the traits that increased yield is reported. Based on marker trait association it appears that some of the QTL are stable across the environments and genetic backgrounds and can be exploited universally.     

QTL analysis of resistance to Fusarium head blight in wheat using a 'Wangshuibai'-derived population

Fusarium head blight (FHB) is a devastating disease that reduces the yield, quality and economic value of wheat. For quantitative trait loci (QTL) analysis of resistance to FHB, F₃ plants and F_3:5 lines, derived from a ‘Wangshuibai’ (resistant)/‘Seri82’(susceptible) cross, were spray inoculated during 2001 and 2002, respectively. Artificial inoculation was carried out under field conditions. Of 420 markers, 258 amplified fragment length polymorphism and 39 simple sequence repeat (SSR) markers were mapped and yielded 44 linkage groups covering a total genetic distance of 2554 cM. QTL analysis was based on the constructed linkage map and area under the disease progress curve. The analyses revealed a QTL in the map interval Xgwm533‐Xs18/m12 on chromosome 3BS accounting for up to 17% of the phenotypic variation. In addition, a QTL was detected in the map interval Xgwm539‐Xs15/m24 on chromosome 2DL explaining up to 11% of the phenotypic variation. The QTL alleles originated from ‘Wangshuibai’ and were tagged with SSR markers. Using these SSR markers would facilitate marker‐assisted selection to improve FHB resistance in wheat.     

Development of cleaved amplified polymorphic sequence (CAPS) markers linked to a green rice leafhopper resistance gene, Grh3(t)

The chromosomal location of the resistance gene for green rice leafhopper (GRLH), an injurious insect for rice, has been determined and RFLP markers closely linked to this gene have been identified. The susceptible japonica rice variety ‘Nipponbare’ was crossed with a resistant japonica rice line ‘Aichi42’, in which green rice leaf hopper resistance had been introduced from an indica variety ‘Rantaj‐emas2’, and the 100 F₂ plants obtained were used for linkage analysis. The green rice leafhopper resistance gene, Grh3(t), was mapped between RFLP markers C288B and C133A on chromosome 6 and co‐segregated with C81. Of the RFLP markers tightly linked to Grh3(t), C81 was converted to a SCAR marker and C133A to a cleaved amplified polymorphic sequence marker that could distinguish the heterozygous genotype to establish an effective marker‐aided selection system for the GRLH resistance gene.     

Efficient application of in vitro anther culture for different European winter wheat (Triticum aestivum L.) breeding programmes

The efficiency of our anther culture protocol was tested with high‐ and low‐responding genotypes, ‘Svilena’ and ‘Berengar’, and 93 F₁ winter wheat crosses in 2010 and 2011. Based on data for these genotypes, the effect of genotype influenced the number of embryo‐like structures, regenerated plantlets and green plantlets, while the number of albino plantlets was affected by genotype, year and environmental factors. Although genotype also influenced the production of green plantlets from breeding crosses, with green plantlets per 100 anthers ranging from 0.04 to 28.67, the average regeneration rate over all crosses was 5.3 green plantlets/100 anthers, which resulted in a total of 11 416 well‐rooted green plantlets. The survival rate of green plantlets following acclimatization was 97.21% in 2010 and 96.34% in 2011. In this study, the phenomenon of albinism and genotype dependency did not hinder the production of more than five thousand green plantlets each year. In our experiments, anther culture proved to be an efficient method in winter wheat breeding programmes with lower costs than alternative technologies.     

RFLP facilitated analysis of tiller and leaf angles in rice (Oryza sativa L.)

Plant type is an important composite trait associated with the yield potential in rice and other cereal crops. Several characters associated with the plant type of modern rice cultivars including tiller angle, leaf and flag leaf angle, were investigated using a complete linkage map with 115 well distributed RFLP markers and progeny testing of 2418 F₂ derived F₄ lines from a cross between O. sativa ssp. japonica cv. ‘Lemont’ and spp. indica cv. ‘Teqing’. One major gene (Ta) and 11 QTLs were largely responsible for the tremendous variation of the three plant type characters in the Lemont/Teqing F₂ population. The major gene, Ta, located between RZ228 and RG667 on chromosome 9, accounted for 47.5% of the phenotypic variation in tiller angle and had large pleiotropic effects on both leaf and flag leaf angles. This gene plus four QTLs accounted for 69.1% of the genotypic variation in tiller angle. Eight additional QTLs for leaf and flag leaf angles were also identified, which collectively explained 52.0 and 66.4% of the genotypic variation of these traits. Ta and three QTLs ( QFla2, QFla5 and QFla7) apparently affected the related plant type characters differently, suggesting their possible differential expression in different developmental stages of rice plants or possibly clustering of different genes affecting these traits. Plant type, and consequently grain yield of rice, may be improved by deliberately manipulating these QTLs in a marker-assisted selection program. This revised version was published online in July 2006 with corrections to the Cover Date.     

New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi,a Saudi landrace into three African cultivars at the reproductive stage

Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems. Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace ‘Hasawi’ as a donor parent to generate three F₂ offspring (consisting each of 500 individuals) with three African cultivars (‘NERICA-L-19’, ‘Sahel 108’ and ‘BG90-2’) used as recipient parents (RP). The F₂s and F_2:3s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F₂-derived offspring, e.g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP’s grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. ‘Hasawi’ contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.     

Cold tolerance during juvenile development in sorghum: a comparative analysis by genomewide association and linkage mapping

Improved cold tolerance during the juvenile phase is a major breeding goal to develop new sorghum cultivars suitable as an alternative energy crop in temperate regions. The objectives of this study were to identify marker‐trait associations for cold tolerance in a sorghum diversity panel fingerprinted with 2620 single nucleotide polymorphism (SNP) markers and to detect quantitative trait loci (QTL) in two F_2:3 populations. Traits of interest were dry matter growth rate (DMGR), leaf appearance rate (LAR), chlorophyll content (SPAD) and chlorophyll fluorescence (F_v′/F_m′ and Ф_PSII) in relation to temperature. The association panel comprised 194 genotypes, while the F_2:3 populations consisted of 80 and 92 genotypes. All populations were tested under controlled conditions in a minimum of four temperature regimes ranging from 9.4°C to 20.8°C. QTL were identified for means across environments and regression parameters describing temperature effects. Several marker‐trait associations for mean (m) DMGR, base temperature (T_b) of SPAD and Ф_PSII and temperature effect on LAR were validated by QTL detected in population 1 or 2. Promising QTL regions were found on chromosomes SBI‐01, SBI‐02, SBI‐03, SBI‐04, SBI‐06 and SBI‐09, among them genomic regions where candidate genes involved in the C‐repeat binding pathway or encoding cold‐shock proteins are located.     

Mapping QTLs related to salinity tolerance of rice at the young seedling stage

Using a population of recombinant inbred lines of the 164 genotypes derived from a cross between ‘Milyang 23’ (indica) and ‘Gihobyeo’ (japonica) in rice (Oryza sativa L.), salt tolerance was evaluated at a young seedling stage in concentrations of 0.5% and 0.7% NaCl. Mapping quantitative trait loci (QTLs) related to salt tolerance was carried out by interval mapping using Qgene 3.0. Two QTLs (qST1 and qST3) conferring salt tolerance at young seedling stage were mapped on chromosome 1 and 3, respectively, and explained 35.5–36.9% of the total phenotypic variation in 0.5% and 0.7% NaCl. The favourable allele of qST1 was contributed by ‘Gihobyeo’, and that of qST3 by ‘Milyang 23’. The results obtained in 0.5% and 0.7% NaCl for 2 years were similar in flanked markers and phenotypic variation.     

Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage

Seed longevity varies considerably in cultivated rice (Oryza sativa L.), but the underlying genetic mechanism of longevity has not been well elucidated. Quantitative trait loci (QTL) that control seed longevity after various periods of seed storage were sought using recombinant inbred lines derived from a combination involving ‘Milyang23’(Indica‐type) and ‘Akihikari’ (Japonica‐type). In all, 12 QTLs for germination and normal seedling growth were detected as indices of seed longevity on chromosome 7 (one region) and chromosome 9 (two regions) in treated seeds that had been stored under laboratory conditions for 1, 2 or 3 years.‘Milyang23’ alleles of all QTLs promoted germination and normal seedling growth after all durations of storage. These QTL regions were detected repeatedly in more than one seed condition. Therefore, we infer that these regions control seed longevity.     

Mapping and validation of the quantitative trait loci for leaf stay‐green‐associated parameters in maize

Functional stay‐green is generally regarded as a desirable trait of varieties in major crops including maize. In this study, we used an F_3:4 recombinant inbred line population with 165 lines from a cross between a stay‐green inbred line (Zheng58) and a model inbred line (B73) using 211 polymorphic simple sequence repeat markers to map quantitative trait loci for three stay‐green‐associated parameters, chlorophyll content, photosystem II photochemical efficiency and stay‐green area, at maturity stage, detected a total of 23 quantitative trait loci (QTL) on nine chromosomes. Single QTL explained 3.7–13.5% of the phenotypic variance. Additionally, we validated some important stay‐green QTL using a heterogeneous inbred family approach and found that the stay‐green‐associated parameters were significantly correlated with the plant yield. This study may contribute to a better insight into the regulatory mechanism behind leaf stay‐green in maize and a novel development of elite maize varieties with delayed leaf senescence through molecular marker‐assisted selection.     

Mapping of quantitative trait loci conferring resistance to bacterial wilt in tobacco (Nicotiana tabacum L.)

Tobacco bacterial wilt (TBW) is one of the most serious tobacco diseases in the world. Studies have shown that tobacco resistance to TBW is quantitatively inherited. This study aimed to map quantitative trait loci (QTL) conferring TBW resistance. An F_2 : 3 population containing 237 lines was developed from a cross between two flue‐cured tobacco cultivars, ‘Yanyan 97’ (YY97; moderately resistant to TBW) and ‘Honghua Dajinyuan’ (HD; highly susceptible to TBW), and a linkage map consisting of 201 simple sequence repeats (SSR) markers and spanning a total length of 2326.7 cM was constructed based on the population. Field experiments were conducted 2011 and 2012, and disease symptoms were investigated three times in each year. The phenotypic data were analysed either separately or jointly for QTL mapping using the software QTLNetwork 2.1. Eight QTL with significant main effects were mapped on chromosomes 2, 6, 12, 17 and 24. A major QTL (qBWR17a) was detected on chromosome 17, which explained up to 30% of the phenotypic variation. The results can facilitate marker‐assisted selection (MAS) in TBW resistance breeding programme.     

杂交粳稻亲本产量性状优异配合力的标记基因型筛选

提高杂交粳稻竞争优势的关键是改良其恢复系产量性状的配合力。为使之更富成效,选用115个SSR引物扩增6个粳稻BT型不育系和12个恢复系的标记基因型,并按NCII遗传设计配制72个F1组合,分析18个亲本的单株日产量、单株有效穗数、每穗总粒数、每穗实粒数、千粒重5个性状的配合力,结合亲本SSR分子标记数据和性状配合力数据筛选了5个性状优异配合力的标记基因型。结果发现20个SSR标记基因型与亲本产量及其构成性状配合力显著相关。其中8个与亲本单个性状配合力相关;6个同时与亲本2个性状配合力相关;4个同时与亲本3个性状配合力相关;2个同时与亲本4个性状配合力相关。同时与多个性状配合力相关的标记基因型,对各性状的作用方向有正有负。RM152-165/170是单株日产量和单株有效穗数优异配合力效应最大的标记基因型,可使F1的相应性状值增加20.6%和12.7%。优异配合力的标记基因型可直接用于粳稻恢复系配合力的分子标记辅助改良。