Identification of Quantitative Trait Loci (QTLs) Affecting Yield and Fiber Properties in Chromosome 16 in Cotton Using Substitution Line

Gossypium hirsutum L. and G. barbadense L. are the two cultivated tetraploid species of cotton. The first is characterized by a high yield and wide adaptation, and the second by its super fiber property. Substitution line in which a pair of intact chromosomes of TM_1 ( G. hirsutum ) were replaced by a pair of homozygous chromosomes of 3_79 ( G. barbadense ) is an excellent material for genetic research and molecular tagging. In this study, substitution line 16 (Sub 16) was used to evaluate the performance of the 16th chromosome in G. barbadense in TM_1 background. The genetic analysis using the major gene plus polygene mixed inheritance model in F 2∶3 family revealed that there might exist 2 QTLs respectively for boll size, lint percentage, lint index, fiber length and the first fruit branch node, 1 QTL for fiber elongation and flowering date, and no QTL for seed index, fiber strength and Micronaire in chromosome 16. However, 9 QTLs (LOD (logarithm of odds)≥3.0) controlling 6 quantitative traits were significantly identified in linkage group of chromosome 16 constructed in (TM_1×3_79) F 2by interval mapping. Among them, 1 QTL for boll size, fiber length, flowering date and fiber elongation could explain 15.2%, 19.7%, 12.1%, and 11.7% phenotypic variance respectively, 2 QTLs for lint index could explain 11.6% and 41.9%, and 3 QTLs for lint percentage could explain 8.7%, 9.6% and 29.2% phenotypic variance respectively. One unlinked SSR marker was associated with one QTL respectively for boll size and flowering date and they could explain 1.60% and 4.63% phenotypic variance. The traits associated significantly with chromosome 16 from Sub 16 were boll weight, lint percentage, lint index, fiber length, fiber elongation and flowering days.

Identification of Wheat-Barley 2H Alien Substitution Lines

The genetic constitution of fifteen materials derived from the cross wheat (Triticum aestivum L. cv. 'Chinese Spring') X barley (Hordeum vulgare L. cv. 'Betzes') was analyzed, and six disomic alien substitution lines were screened by GISH. The chromosome configurations in pollen mother cells at meiotic metaphase I (PMCs M I) of F, from each disomic substitution line respectively crossed with double ditelocentric lines 2A, 2B and 2D of 'Chinese Spring' were observed, and a set of wheat-barley disomic alien substitution lines 2H(A), 2H(B) and 2H(D) were obtained. The RFLP analysis with the probe psr131 on the short arm of wheat homeologous group 2 combining with four restriction enzymes were carried out. The results indicated that the probe psr131 could be used as molecular marker to tag the barley chromosome 2H. The barley chromosome 2H had good genetic compensation ability for wheat chromosomes 2B and 2D in vitality and other agronomic characters. The result of testing seed was that the wheat appearance starch quality had been changed from the half-farinaceous of 'Chinese Spring' to the half-cutin of substitution lines by transferring the barley chromosome 2H to wheat.

Mapping of QTLs Related to Grain Weight Using Chromosome Single Segment Substitution Lines in Rice

Grain weight, one of the major factors determining rice yield, is a typical quantitative trait control ed by multiple genes. With Guangluai 4 as recipient and Nipponbare as donor, a population of 119 chromosome single segment substitution lines had been developed. Correlation analysis between grain weight and grain shape by SPSS revealed that 1 000-grain weight shared extremely significant posi-tive correlation with grain length and length-width ratio, but no significant correlation with grain width and thickness. The QTL analysis of grain weight was carried out using one-way analysis of variance and Dunnett＇s test. Nineteen stable QTLs re-sponsible for grain weight were identified over two years. Al 19 QTLs were identi-fied on al chromosomes except for chromosome 10 and 12 at a significance level of P≤0.001. Among them, 10 QTLs had a positive effect and were derived from the Nipponbare al ele, the additive effect of these QTLs ranged from 0.49 to 2.74 g, and the contributions of the additive effects ranged from 2.00% to 11.05%. Another 9 QTLs had a negative effect and were al derived from Guangluai 4 al ele, the ad-ditive effect of these QTLs ranged from 0.60 to 2.35 g, and the contributions of the additive effects ranged from 2.40% to 9.84%. The results provide a basis for the fine mapping and gene cloning of novel locus associated with rice grain weight.

QTLs Mapping for Salinity Tolerance at Seedling Stage or Rice(Oryza sativa L.) Using Chromosome Segment Substitution Lines

In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for salt tolerance under the salt stress simulated with 0.5% NaCI, using survival rate as the index. The data were analyzed by QTL IciMapping v3.1, and the results showed that one QTL （QSsr3） related to salt tolerance was located in the vicinity of the marker RM1350 on chromosome 3, into a genetic interval of 113.2-132.8 cM, with a contribution rate of 17.75%. The additive effect was 10.9, indicating that the QTL derived from the parent Nipponbare improved the salt tolerance of rice at seedling stage. This study will provide a theoretical basis for the selection of salt tolerant rice germplasm.

Mapping QTLs Associated with Sheath Blight Resistance Using Chromosome Segment Substitution Lines of Rice(Oryza sativa L.)

In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with sheath blight resis-tance in rice with toothpick inoculation method. A total of three sheath blight resis-tance-associated QTLs （qsb8-1, qsb8-2 and qsb8-3） were identified, which were lo-cated on adjacent molecular markers RM3262, RM5485 and RM3496 of chromo-some 8; the genetic interval was 81.7cM-91.7cM, 91.7cM-108.1cM and 108.1cM-119.6cM, respectively. The additive effect of qsb8-2 was negative, indicating that sheath blight resistance of susceptible parent harboring qsb8-2 fragment was en-hanced; additive effects of qsb8-1 and qsb8-3 were positive, indicating that sheath blight resistance of susceptible parent harboring qsb8-1 and qsb8-3 fragments was reduced.

Identification of QTLs for Plant Height and Its Components by Using Single Segment Substitution Lines in Rice (Oryza sativa)

QTLs for plant height and its components on the substituted segments of fifty-two single segment substitution lines （SSSLs） in rice were identified through t-test （P〈0.001） for comparison between each SSSL and recipient parent Huajingxian 74. On the 14 substituted segments, 24 QTLs were detected, 10 for plant height, 2 for panicle length, 4 for length of the first internode from the top, 5 for length of the second internode from the top and 3 for length of the third internode from the top, respectively. All these QTLs were distributed on nine rice chromosomes except chromosomes 5, 9 and 11. The additive effect ranged from -4.08 to 3.98 cm, and the additive effect percentages varied from -19.35% to 10.43%.

Detection of QTL for Cold Tolerance at Bud Bursting Stage Using Chromosome Segment Substitution Lines in Rice (Oryza sativa)

Ab The cold tolerance at the bud bursting stage （CTB） was evaluated at 5℃ by using a set of 95 chromosome segment substitution lines （CSSLs） derived from an indica rice 9311 and a japonica rice Nipponbare with a genetic background of 9311. The result showed that six CSSLs had slightly stronger effect on CTB than 9311. Total four quantitative trait loci （QTLs） for CTB were preliminary mapped on chromosomes 5 and 7 by substitution mapping, qCTB-5-1, qCTB-5-2 and qCTB-5-3 were mapped in the region of RM267-RM1237, RM2422-RM6054 and RM3321-RM1054, which were 21.3 cM, 27.4 cM and 12.7 cM in genetic distance on rice chromosome 5, respectively, qCTB-7 was mapped in a 6.8-cM region of RM11-RM2752 on rice chromosome 7.

Unconditional and Conditional QTL Mapping for Tiller Numbers at Various Stages with Single Segment Substitution Lines in Rice(Oryza sativa L.)

Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice. It is important to understand ＂static＂ and ＂dynamic＂ information of the QTLs for tillers in rice. This work was the first time to simultaneously map unconditional and conditional QTLs for tiller numbers at various stages by using single segment substitution lines in rice. Fourteen QTLs for tiller number, distributing on the corresponding substitution segments of chromosomes 1, 2, 3, 4, 6, 7 and 8 were detected. Both the number and the effect of the QTLs for tiller number were various at different stages, from 6 to 9 in the number and from 1.49 to 3.49 in the effect, respectively. Tiller number QTLs expressed in a time order, mainly detected at three stages of 0-7 d, 14-21 d and 35-42 d after transplanting with 6 positive, 9 random and 6 negative expressing QTLs, respectively. Each of the QTLs expressed one time at least during the whole duration of rice. The tiller number at a specific stage was determined by sum of QTL effects estimated by the unconditional method, while the increasing or decreasing number in a given time interval was controlled by the total of QTL effects estimated by the conditional method. These results demonstrated that it is highly effective and accurate for mapping of the QTLs by using single segment substitution lines and the conditional analysis methodology.

Development and identification of a dwarf wheat-Leymus mollis double substitution line with resistance to yellow rust and Fusarium head blight

Leymus mollis (Trin.) Pilger (2n = 4x = 28, NsNsXmXm,), a wild relative of common wheat, possesses many potentially valuable traits for genetic improvement of wheat, including strong, short stems, long spikes with numerous spikelets, tolerance to drought and cold stresses, and resistance to many fungal and bacterial diseases. In the present study, a wheat-L. mollis double substitution line DM96 was selected from a F6 progeny of a cross between M842-16 (an octoploid Tritileymus line) and D4286 (a Triticum durum line) using genomic in situ hybridization (GISH), simple sequence repeat (SSR) markers, and expressed sequence tagged sequence site (EST-STS) markers. Chromosome analysis at mitosis and meiosis showed that DM96 had a chromosome constitution of 2n = 42 = 21II. GISH analysis indicated that DM96 carried 38 chromosomes from wheat and two homologous pairs of Ns chromosomes from L. mollis. Fluorescent in situ hybridization (FISH) showed that chromosomes 2Ns and 3Ns from L. mollis had replaced wheat chromosomes 2D and 3D in DM96, which was confirmed by SSR and STS markers. The newly developed substitution line DM96 has shorter height, longer spikes and more kernels than its parents and showed high resistance to stripe rust and Fusarium head blight (FHB). Thus, this line is a new bridge material for the production of useful translocation lines for wheat genetic research and genetic improvement of wheat yield and disease resistance in breeding programs.

Identification of Multiple Alleles at the Wx Locus and Development of Single Segment Substitution Lines for the Alleles in Rice

The microsatellite markers 484/485 and 484/W2R were used to identify the multiple alleles at the Wx locus in rice germplasm. Fifteen alleles were identified in 278 accessions by using microsatellite class and G-T polymorphism. Among these alleles, （CT）12-G, （CT）15-G, （CT）16-G, （CT）17-G, （CT）18-G and （CT）21-G have not been reported. Seventy-two single-segment substitution lines （SSSLs） carrying different alleles at the Wx locus were developed by using Huajingxian 74 with the （CT）11-G allele as a recipient and 20 accessions containing 12 different alleles at the Wx locus as donors. The estimated length of the substituted segments ranged from 2.2 to 77.3 cM with an average of 17.4 cM.

Identification of QTL for kernel number-related traits in a rice chromosome segment substitution line and fine mapping of qSP1

A chromosome segment substitution line (CSSL) is a powerful tool for combining quantitative trait locus (QTL) mapping with the pyramiding of desirable alleles. The rice CSSL Z1364 with increased kernel number was identified in a BC3F8 population derived from a cross of Nipponbare as the recipient with Xihui 18 as the donor parent. Z1364 carried three substitution segments distributed on chromosomes 1, 6, and 8. The mean substitution length was 1.19 Mb. Of 17 QTL identified on the substitution segments, qSP1 for spikelets per panicle, qSSD1 for seed-set density, and qNSB1 for number of secondary branches explained respectively 57.34%, 87.7%, and 49.44% of the corresponding phenotypic variance and were all linked to RM6777. Chi-square analysis showed that the increased kernel number in Z1364 was inherited recessively by a single gene. By fine mapping, qSP1 was delimited to a 50-kb region on the short arm of chromosome 1. Based on DNA sequence, a previously uncharacterized rice homolog of Arabidopsis thaliana AT4G32551 was identified as a candidate gene for qSP1 in which mutation increases the number of spikelets and kernels in Z1364. qSP1 was expressed in all tissues, but particularly in 1-cm panicles. The expression levels of OsMADS22, GN1A, and DST were upregulated and those of LAX2, GNP1, and GHD7 were downregulated in Nipponbare. These results provide a foundation for functional research on qSP1.

Identification of long-grain chromosome segment substitution line Z744 and QTL analysis for agronomic traits in rice

Length of grain affects the appearance, quality, and yield of rice. A rice long-grain chromosome segment substitution line Z744, with Nipponbare as the recipient parent and Xihui 18 as the donor parent, was identified. Z744 contains a total of six substitution segments distributed on chromosomes(Chrs.) 1, 2, 6, 7, and 12, with an average substitution length of 2.72 Mb. The grain length, ratio of length to width, and 1 000-grain weight of Z744 were significantly higher than those in Nipponbare. The plant height, panicle number, and seed-set ratio in Z744 were significantly lower than those in Nipponbare, but they were still 78.7 cm, 13.5 per plant, and 86.49%, respectively. Furthermore, eight QTLs of different traits were identified in the secondary F2 population, constructed by Nipponbare and Z744 hybridization. The grain weight of Z744 was controlled by two synergistic QTLs(qGWT1 and q GWT7) and two subtractive QTLs(qGWT2 and qGWT6), respectively. The increase in the grain weight of Z744 was caused mainly by the increase in grain length. Two QTLs were detected, qGL1 and qGL7-3, which accounted for 25.54 and 15.58% of phenotypic variation, respectively. A Chi-square test showed that the long-grain number and the short-grain number were in accordance with the 3:1 separation ratio, which indicates that the long grain is dominant over the short-grain and Z744 was controlled mainly by the principal effect qGL1. These results offered a good basis for further fine mapping of qGL1 and further dissection of other QTLs into single-segment substitution lines.

Development of Chromosomal Segment Substitution Lines from a Backcross Recombinant Inbred Population of Interspecific Rice Cross

A backcross recombinant inbred line population consisting of 202 lines was developed from Xieqingzao B//Xieqingzao B / Dongxiang wild rice. The population was assayed with DNA markers and phenotyped on planthopper resistance and yield traits. A linkage map consisting of 119 DNA markers and spanned for 1188 cM over the 12 rice chromosomes was constructed. Thirty-two chromosomal segment substitution lines were selected based on the percentage of Xieqingzao B allele at marker loci. These lines are of great potential for gene mapping and alien gene introgression.

QTL Mapping for Rice RVA Properties Using High-Throughput Re-sequenced Chromosome Segment Substitution Lines

The rapid visco analyser （RVA） profile is an important factor for evaluation of the cooking and eating quality of rice. To improve rice quality, the identification of new quantitative trait loci （QTLs） for RVA profiling is of great significance. We used a japonica rice cultivar Nipponbare as the recipient and indica rice 9311 as the donor to develop a population containing 38 chromosome segment substitution lines （CSSLs） genotyped by a high-throughput re-sequencing strategy. In this study, the population and the parent lines, which contained similar apparent amylose contents, were used to map the QTLs of RVA properties including peak paste viscosity （PKV）, hot paste viscosity （HPV）, cool paste viscosity （CPV）, breakdown viscosity （BKV）, setback viscosity （SBV）, consistency viscosity （CSV）, peak time （PET） and pasting temperature （PAT）. QTL analysis was carried out using one-way analysis of variance and Dunnett＇s test, and stable QTLs were identified over two years and under two environments. We identified 10 stable QTLs： qPKV2-1, qSBV2-1; qPKV5-1, qHPV5-1, qCPV5-1; qPKV7-1, qHPV7-1, qCPV7-1, qSBV7-1; and qPKV8-1 on chromosomes 2, 5, 7 and 8, respectively, with contributions ranging from -95.6% to 47.1%. Besides, there was pleiotropy in the QTLs on chromosomes 2, 5 and 7.

QTL Detection for Rice Grain Shape Using Chromosome Single Segment Substitution Lines

Rice grain shape is one of the important factors affecting grain quality and yield,but it is liable to be influenced by genetic backgrounds and environments.The chromosome single segment substitution lines(SSSLs) in rice have been considered as ideal populations to identify the quantitative trait loci(QTLs).In this study,22 QTLs affecting rice grain shape were detected to be distributed on eight chromosomes except chromosomes 6,9,11 and 12 by using SSSLs.Among them,seven QTLs conditioned grain length,six conditioned grain width,five affected grain length-width ratio and four controlled grain thickness.

Development and genetic analysis of wheat double substitution lines carrying Hordeum vulgare 2H and Thinopyrum intermedium 2Ai#2 chromosomes

Thinopyrum intermedium and barley are two close relatives of wheat and carry many genes that are potentially valuable for the improvement of various wheat traits. In this study we created wheat double substitution lines by hybridizing different wheat–Th. intermedium and wheat–barley disomic alien substitution lines, with the aim of using genes in Th. intermedium and barley for wheat breeding and investigating the genetic behavior of alien chromosomes and their wheat homoeologs. As expected, we obtained two types of wheat double substitution lines,2D2Ai#2(2B)2H( A) and 2A2 Ai#2(2B)2H(2D), in which different group 2 wheat chromosomes were replaced by barley chromosome 2 H and Th. intermedium chromosome 2Ai#2. The new materials were characterized using molecular markers, genomic in situ hybridization(GISH), and fluorescent in situ hybridization(FISH). GISH and FISH experiments revealed that the double substitution lines harbor 42 chromosomes including 38 wheat chromosomes, a pair of barley chromosomes, and a pair of Th. intermedium chromosomes. Analysis using specific DNA markers showed that two pairs of wheat homoeologous group 2 chromosomes in the new lines were substituted by a pair of 2H and a pair of 2Ai#2 chromosomes. Chromosome 2H showed a higher transmission rate than 2Ai#2, and both chromosomes were preferentially transmitted between generations via female gametes. Evaluation of botanic and agronomic traits demonstrated that,compared with their parents, the new lines showed similar growth habits and plant type but differences in plant height, flowering date, and self-fertility. Cytological observations using different probes suggested that the double substitution lines showed nearly normal genetic behavior before and during meiosis. The novel substitution lines can potentially be used in wheat meiosis research and breeding programs.

Identification of Differentially Expressed Genes Associated with Cotton Fiber Development in a Chromosomal Substitution Line(CS-B22sh)

One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-

Evaluation of Agronomic Traits in Chromosome Segment Substitution Lines of KDML105 Containing Drought Tolerance QTL under Drought Stress

Drought is a major abiotic constraint to rice production in rainfed lowland and insufficiently irrigated areas. The improvement of drought tolerant varieties is one of the strategies to reduce the negative effects of drought. Quantitative trait loci （QTLs） for primary and secondary traits related to drought tolerance （DT） on chromosomes 1, 3, 4, 8 and 9 that determined from double haploid lines derived from a cross between CT9993 and IR62266 were introgressed and dissected into small pieces in the genetic background of Khao Dawk Mall 105 （KDML105） to develop chromosome segment substitution line （CSSL） population. The CSSLs were evaluated at the reproductive stage for their agronomic performance and yield components under drought stress, and results were compared with irrigated condition. The flowering of CSSL lines was 6 to 7 d earlier than KDML105. The mean values of grain yields in the CSSLs were higher than KDML105 under drought and irrigated conditions. At irrigated condition, the grain yields of introgression lines carrying DT-QTLs from chromosomes 4 and 8 were higher than that of KDML105, whereas other traits showed little difference with KDML105. Analysis indicated that grain yield has positive correlation with plant height, tiller and panicle number per plant, and total grain weight per plant under drought stress while negatively correlated with days to flowering. As mentioned above, CSSLs showing good adaptation under drought stress can be used as genetic materials to improve drought tolerance in Thai rainfed lowland rice breeding program, and as materials to dissect genes underlying drought tolerance.

Characterization of chromosome segment substitution lines reveals candidate genes associated with the nodule number in soybean

Soybean is one of the most important food crops worldwide.Like other legumes,soybean can form symbiotic relationships with Rhizobium species.Nitrogen fixation of soybean via its symbiosis with Rhizobium is pivotal for sustainable agriculture.Type Ⅲ effectors(T3Es)are essential regulators of the establishment of the symbiosis,and nodule number is a feature of nitrogen-affected nodulation.However,genes encoding T3Es at quantitative trait loci(QTLs)related to nodulation have rarely been identified.Chromosome segment substitution lines(CSSLs)have a common genetic background but only a few loci with heterogeneous genetic information;thus,they are suitable materials for identifying candidate genes at a target locus.In this study,a CSSL population was used to identify the QTLs related to nodule number in soybean.Single nucleotide polymorphism(SNP)markers and candidate genes within the QTLs interval were detected,and it was determined which genes showed differential expression between isolines.Four candidate genes(GmCDPK28,GmNAC1,GmbHLH,and GmERF5)linked to the SNPs were identified as being related to nodule traits and pivotal processes and pathways involved in symbiosis establishment.A candidate gene(GmERF5)encoding a transcription factor that may interact directly with the T3E NopAA was identified.The confirmed CSSLs with important segments and candidate genes identified in this study are valuable resources for further studies on the genetic network and T3Es involved in the signaling pathway that is essential for symbiosis establishment.

Interspecific Chromosome Substitution Lines as Genetic Resources for Improvement,Trait Analysis and Genomic Inference

The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of