Single Mendelian Factor Research Articles

Exome Sequencing from Bulked Segregant Analysis Identifies a Gene for All-Stage Resistance to Stripe Rust on Chromosome 1AL in Chinese Wheat Landrace 'Xiaohemai'.

Stripe rust caused by Puccinia striiformis f. sp. tritici is one of the most destructive diseases of wheat. Identifying novel resistance genes applicable for developing disease-resistant cultivars is important for the sustainable control of wheat stripe rust. Chinese wheat landrace 'Xiaohemai' ('XHM') is an elite germplasm line with all-stage resistance (ASR) effective against predominant Chinese P. striiformis f. sp. tritici races. In this study, we performed a bulked segregant analysis coupled with exome capture sequencing (BSE-seq) to identify a candidate genomic region strongly associated with stripe rust resistance on chromosome 1AL in 173 F2:3 lines derived from the cross 'XHM' × 'Avocet S'. The gene, designated as YrXH-1AL, was validated by a conventional quantitative trait locus analysis using newly developed Kompetitive allele-specific PCR (KASP) markers, explaining up to 48.50% of the phenotypic variance. By testing a secondary mapping population comprising 144 lines from the same cross at the seedling stage with prevalent P. striiformis f. sp. tritici race CYR34, YrXH-1AL was identified as a single Mendelian factor in a 1.5-cM interval flanked by KASP markers KP1A_484.33 and KP1A_490.09. This region corresponded to a 5.76-Mb genomic interval on 'Chinese Spring' chromosome 1AL. Furthermore, two cosegregating KASP markers showed high polymorphisms among 130 Chinese wheat cultivars and could be used for marker-assisted selection. Because no other Yr genes for ASR that originated from common wheat have been detected on chromosome 1AL, YrXH-1AL is likely a novel gene that can be incorporated into modern breeding materials to develop wheat cultivars with enhanced stripe rust resistance.

Eragrostis curvula, a Model Species for Diplosporous Apomixis.

Eragrostis curvula (Schrad.) Ness is a grass with a particular apomictic embryo sac development called Eragrostis type. Apomixis is a type of asexual reproduction that produces seeds without fertilization in which the resulting progeny is genetically identical to the mother plant and with the potential to fix the hybrid vigour from more than one generation, among other advantages. The absence of meiosis and the occurrence of only two rounds of mitosis instead of three during embryo sac development make this model unique and suitable to be transferred to economically important crops. Throughout this review, we highlight the advances in the knowledge of apomixis in E. curvula using different techniques such as cytoembryology, DNA methylation analyses, small-RNA-seq, RNA-seq, genome assembly, and genotyping by sequencing. The main bulk of evidence points out that apomixis is inherited as a single Mendelian factor, and it is regulated by genetic and epigenetic mechanisms controlled by a complex network. With all this information, we propose a model of the mechanisms involved in diplosporous apomixis in this grass. All the genetic and epigenetic resources generated in E. curvula to study the reproductive mode changed its status from an orphan to a well-characterised species.

Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis)

BackgroundLeaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation.ResultsIn this study, we identified a stably inherited yellow leaf mutant derived from ‘Huaguan’ pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm.ConclusionsOur study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.

Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.).

KEY MESSAGE: cqSW.A03-2, one of the six identified quantitative trait loci associated with thousand-seed weight in rapeseed, is mapped to a 61.6-kb region on chromosome A03 and corresponds to the candidate gene BnaA03G37960D. Seed weight is an important factor that determines the seed yield of oilseed rape (Brassica napus L.). To elucidate the genetic mechanism of thousand-seed weight (TSW), quantitative trait locus (QTL) mapping was conducted using a double haploid population derived from the cross between an elite line ZY50 and a pol cytoplasmic male sterility restorer line 7-5. The genetic basis of TSW was dissected into six major QTLs. One major QTL denoted as cqSW.A03-2, which explained 8.46-13.70% of the phenotypic variation, was detected across multiple environments. To uncover the genetic basis of cqSW.A03-2, a set of near-isogenic lines were developed. Based on the test of self-pollinated progenies, cqSW.A03-2 was identified as a single Mendelian factor and the ZY50 allele at cqSW.A03-2 showed a positive effect on TSW. Fine mapping delimited the cqSW.A03-2 locus into a 61.6-kb region, and 18 genes within this region were predicted. Candidate gene association analysis and expression analysis indicated that a histidine kinase gene (BnaA03G37960D) is likely to be the candidate gene for the cqSW.A03-2 locus. Our results may contribute to a better understanding of the molecular mechanism of seed weight regulation and promote the breeding program for yield improvement in rapeseed.

Identification and fine mapping of a major locus controlling branching in Brassica napus

A candidate branching-controlling gene for qDBA09 was identified after delimiting a Brassica napus recessive locus within a 270-kb interval on chromosome A09. Although branching is an important trait associated with the adaptation and yield potential of rapeseed (Brassica napus), the genetic mechanisms underlining branching in this crop remain poorly understood. In this study, we characterized a naturally occurring rapeseed mutant, db1, which showed an ultrahigh branching density phenotype. By combining bulked segregant analysis (BSA) and the Brassica 60K SNP BeadChip Array, we identified two major quantitative trait loci (QTLs), qDBA09 and qDBC06, which were subsequently confirmed using the traditional QTL-mapping approach. Analysis of 208 individuals from a BC1F3 population indicated that the qDBA09 locus is a single Mendelian factor and that the dense branching phenotype is controlled by a single recessive gene. Furthermore, QTL analysis confirmed that qDBA09 explained between 9.5 and 70.5% of the variation in branching-related traits. Using 7785 individuals from the BC1F3 population, we mapped qDBA09 to a DNA fragment of approximately 270kb in length that contained 27 predicted genes, three of which were identified as potentially involved in the control of the dense branching trait. Based on the reported function of these genes, together with sequence comparisons and co-segregation analysis, we identified a potential candidate gene for the qDBA09 locus. The present findings lay the foundations for further in-depth research on the branching mechanisms of B. napus.

Fine mapping of a silique length- and seed weight-related gene in Brassica napus.

Using microarray analysis combined with map-based cloning, a major locus positively regulating SL and SW was mapped to a 98.47kb interval on A09 in rapeseed. In rapeseed, seed yield is closely associated with silique-related traits such as silique length (SL) and seed weight (SW). Previously identified quantitative trait loci (QTLs) revealed that SL and SW are complex traits and many QTLs overlap. However, the genetic characterization of the association between SL and SW is poorly understood. In the present study, a BC3F3 near isogenic line developed from a short silique plant and the long silique cultivar 'ZS11' was analyzed to identify the locus related to SL. Map-based cloning indicated that a major locus acting as a single Mendelian factor was mapped to a 98.47kb region on chromosome A09. BLAST analysis and DNA sequencing showed SNP variations and a fragment replacement in the upstream region of the candidate gene BnaA09g55530D may alter gene expression and influence SL. The results showed that this SL locus may also positively affect SW as well as in the 186 rapeseed accessions identified by the associated markers. Therefore, selecting plants with appropriate SL and developing functional markers for the associated gene could play important roles in the molecular breeding of high-yield rapeseed varieties.

Miniscule differences between sex chromosomes in the giant genome of a salamander

In the Mexican axolotl (Ambystoma mexicanum), sex is determined by a single Mendelian factor, yet its sex chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess a single sex-determining locus. As sex chromosomes are theorized to differentiate rapidly, species with undifferentiated sex chromosomes provide the opportunity to reconstruct early events in sex chromosome evolution. Whole genome sequencing of 48 salamanders, targeted chromosome sequencing and in situ hybridization were used to identify the homomorphic sex chromosome that carries an A. mexicanum sex-determining factor and sequences that are present only on the W chromosome. Altogether, these sequences cover ~300 kb of validated female-specific (W chromosome) sequence, representing ~1/100,000th of the 32 Gb genome. Notably, a recent duplication of ATRX, a gene associated with mammalian sex-determining pathways, is one of few functional (non-repetitive) genes identified among these W-specific sequences. This duplicated gene (ATRW) was used to develop highly predictive markers for diagnosing sex and represents a strong candidate for a recently-acquired sex determining locus (or sexually antagonistic gene) in A. mexicanum.

Two Contrasting Patterns and Underlying Genes for Coadaptation of Seed Dormancy and Flowering Time in Rice

Association between seed dormancy (SD) and flowering time (FT) may generate a synergy in plant adaptation. This research aimed to identify patterns and underlying genes of the association in rice (Oryza sativa). Four F2 and two BC1F1 populations from crosses of weedy/cultivated rice, and two families of progeny lines from backcrosses were evaluated for variations in time to flowering and germination ability. The two measurements were correlated negatively in the F2 and BC1F1 populations, but positively in advanced generations of the progeny lines. The negative correlations were resulted from linkage disequilibria between SD and FT loci at 7–40 cM apart. The positive correlations arose from co-located SD and FT loci undetectable in the BC1F1 population. Two independent sets of co-localized loci were isolated as single Mendelian factors, and haplotypes that promote flowering and reduce germination derived from weedy and cultivated rice, respectively. The presence of negative and positive correlations indicates that the rice complex has maintained two contrasting patterns of SD-FT coadaptation, with the positive being “recessive” to the negative pattern. Modeling with isogenic lines suggests that a negative pattern could generate a greater synergy (difference between haplotype variants) than the positive one for seedbank persistence, or enhanced plant adaptation to seasonal changes in temperature or moisture. However, the early-flowering dormant genotype of a positive pattern could also have a selective advantage over its counterpart for weeds to avoid harvesting. The isolated haplotypes could be used to manipulate cultivars simultaneously for germination ability and growth duration.

A plant biodiversity effect resolved to a single chromosomal region.

SummaryDespite extensive evidence that biodiversity promotes plant community productivity, progress towards understanding the mechanistic basis of this effect remains slow, impeding the development of predictive ecological theory and agricultural applications. Here, we analysed non-additive interactions between genetically divergent Arabidopsis accessions in experimental plant communities. By combining methods from ecology and quantitative genetics, we identified a major effect locus at which allelic differences between individuals increase above-ground productivity of communities. In experiments with near-isogenic lines, we show that this diversity effect acts independently of other genomic regions and can be resolved to a single region representing less than 0.3% of the genome. Using plant-soil-feedback experiments, we also demonstrate that allelic diversity causes genotype-specific soil legacy responses in a consecutive growing period, even after the original community has disappeared. Our work thus suggests that positive diversity effects can be linked to single Mendelian factors, and that a range of complex community properties can have a simple cause. This may pave the way to novel breeding strategies, focussing on phenotypic properties that manifest themselves beyond isolated individuals, i.e. at a higher level of biological organisation.

QSE7 is a major quantitative trait locus (QTL) influencing stigma exsertion rate in rice (Oryza sativa L.)

Stigma exsertion is a key determinant to increase the efficiency of commercial hybrid rice seed production. The major quantitative trait locus (QTL) qSE7 for stigma exsertion rate was previously detected on the chromosome 7 using 75 Chromosome Segment Substitution Lines (CSSLs) derived from a cross between the high stigma exsertion indica maintainer XieqingzaoB (XQZB) and low stigma exsertion indica restorer Zhonghui9308 (ZH9308). The C51 line, a CSSL population with an introgression from XQZB, was backcrossed with ZH9308 to produce the secondary F2 (BC5F2) and F2:3 (BC5F2:3) populations. As a result, the Near Isogenic Line (NIL qSE7XB) was developed. Analysis indicated qSE7 acted as a single Mendelian factor and decreased the stigma exsertion. We hypothesized qSE7 regulates single, dual, and total stigma exsertion rate, provided experimental support. qSE7 was mapped and localized between RM5436 and RM5499 markers, within a physical distance of 1000-kb. With use of new insertion-deletion (InDel) markers and analysis of the heterozygous and phenotypic data, it was ultimately dissected to a 322.9-kb region between InDel SER4-1 and RM5436. The results are useful for additional identification and isolation of this candidate gene controlling stigma exsertion rate, and provide a basis for further fine mapping, gene cloning, and Marker Assisted Selection (MAS) breeding later.

Genetic Dissection of the Major Quantitative Trait Locus (qSE11), and Its Validation As the Major Influence on the Rate of Stigma Exsertion in Rice (Oryza sativa L.).

The rate of stigma exsertion (SE) is an important trait in rice breeding because the efficiency of hybrid rice seed production can be improved by increasing the percentage of stigmas that exsert. In this study, we developed a near isogenic line (NIL) from two parents, XieqingzaoB (XQZB) and Zhonghoi9308 (ZH9308), which have high and low SE rates in that order. In our previous study, we employed 75 chromosome segment substitution lines (CSSLs) and analyzed quantitative trait loci (QTLs) for their influence on SE rate. The single gene QTL (qSE11), which is located on chromosome 11, was responsible for this trait. In this study, we focused on one of the CSSLs (C65), namely, the NIL (qSE11XB). It contains an introgression segment of XQZB in the genetic background of ZH9308, and exhibits a significantly higher SE rate than that of the parents. We demonstrated that qSE11 regulated both the single and the dual SE rates. They both contribute to the total SE rate. Genetic analysis revealed that qSE11 acted as a single Mendelian factor and that the allele from XQZB increased the SE rate. The validity of our conclusions was established when C65 was used to develop secondary F2 (BC5F2) and F2:3 (BC5F2:3) populations by backcrossing to ZH9308, with subsequent selfing. We entered 3600 plants from the F2 population and 3200 from the F2:3 populations into a genetic dissection program and dissected the major QTL qSE11 to a 350.7-kb region located on chromosome 11. This study will contribute to the future isolation of candidate genes of SE and will play a vital role in future hybrid rice seed production programs.

Root‐specific expression of opine genes and opine accumulation in some cultivars of the naturally occurring genetically modified organism Nicotiana tabacum

Previous studies have shown that Nicotiana tabacum contains three Agrobacterium-derived T-DNA sequences inherited from its paternal ancestor Nicotiana tomentosiformis. Among these, the TB locus carries an intact mannopine synthase 2' gene (TB-mas2'). This gene is similar to the Agrobacterium rhizogenes A4-mas2' gene that encodes the synthesis of the Amadori compound deoxyfructosyl-glutamine (DFG or santhopine). In this study we show that TB-mas2' is expressed at very low levels in N.tomentosiformis and in most N.tabacum cultivars; however, some cultivars show high TB-mas2' expression levels. The TB-mas2' promoter sequences of low- and high-expressing cultivars are identical. The low/high level of expression segregates as a single Mendelian factor in a cross between a low- and a high-expression cultivar. pTB-mas2'-GUS and pA4-mas2'-GUS reporter genes were stably introduced in N.benthamiana. Both were mainly expressed in the root expansion zone and leaf vasculature. Roots of tobacco cultivars with high TB-mas2' expression contain detectable levels of DFG.

Fine mapping of DTH3b, a minor heading date QTL potentially functioning upstream of Hd3a and RFT1 under long-day conditions in rice

Flowering time or heading date in rice is an important agronomic trait that determines cultivation area and cropping season of a given variety. The genes/loci that have minor effect on the heading date are believed to play a critical role in adaptation of rice to different geographical regions and are preferred by breeders. Previously, we detected a stable minor-effect quantitative trait locus, qDTH-3b (for Days to heading 3b; hereafter referred to as DTH3b), using a small population consisting of recombinant inbred lines derived from a cross between the japonica cv. Asominori (Aso) and the indica cv. IR24. However, its precise location remains to be defined. In this study, we fine-mapped DTH3b by using advanced backcrossing lines and explored its role in regulating the heading date. First, we constructed a BC4F2 population by backcrossing a chromosome segment substitution line (CSSL23) with Aso as a recurrent parent. Then, we developed a near-isogenic line (NIL) from this population by marker-assisted selection. This NIL has the genetic background of Aso but carries a 12-cM DTH3b-containing chromosome segment from IR24. Compared with Aso, the NIL showed 6.9-day delay in flowering time and 63.8 % lower seed maturation rate under long-day (LD) conditions, whereas there was no significant difference between the NIL and Aso under short-day conditions. Using a total of 1500 Asominori/NIL F2:3 or F3:4 late-heading families grown under LD conditions, we finally dissected DTH3b to a single Mendelian factor and delimited it to a 46-kb genomic region which contains seven open reading frames. Further, our quantitative real-time PCR analysis indicated that transcription level of Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T 1), the two florigen genes, was significantly lower in the NIL than in Aso, suggesting that DTH3b functions upstream of Hd3a and RFT1 under LD conditions. We propose that DTH3b Aso positively regulates flowering time and contributes to adaptation of rice to the north. Cloning and then manipulation of DTH3b can be a useful approach to optimize flowering time in rice breeding.

Identification and fine mapping of qPH6, a novel major quantitative trait locus for plant height in rice

Plant height is one of the determinants that influence rice plant architecture and grain yield. Identification of useful novel genes related to plant height is necessary for breeding high-yield rice. In this study, C33084, a backcross introgression line derived from a japonica cultivar (Balilla) as the recurrent parent and an indica cultivar (Dular) as the donor parent, was employed to characterize a novel major quantitative trait locus with a large effect on plant height in rice. C33084 showed a significantly higher plant height than Balilla. Genetic analysis of the F2 and F4 generations deriving from a cross between C33084 and Balilla revealed that this phenotypic variation was controlled by a single Mendelian factor, qPH6, which is located on the long arm of chromosome 6. The recessive allele, qph6, from Balilla has a negative effect on plant height. Fine mapping was carried out with a total of 1,791 recessive individuals from the F2 and F4 generations, and the gene was delimited to a ~41-kb region containing three annotated genes according to available sequence annotation databases. This information could be helpful for future identification and isolation of the candidate genes. Phenotypic evaluation of the near isogenic lines NIL (qPH6) and NIL (qph6) suggested that qPH6 has no pleiotropic effect on other traits. The discovery of qPH6 might be useful for the design and breeding of crops with high grain yield and quality.

Mapping and candidate gene identification defining BnChd1-1, a locus involved in chlorophyll biosynthesis in Brassica napus

The chlorophyll-deficient mutant (Bnchd1) is a spontaneous mutant of Brassica napus. Compared with the wild type, ‘Qingyou 10’, Bnchd1 exhibits distinct phenotypes, including interveinal yellowing leaves at the seedling stage and light-green leaves at the bolting stage, dwarfism throughout the lifespan, extremely low seed yields and abnormally shaped and early degradation of chloroplasts. Defective chloroplasts significantly reduce the levels of pigment in Bnchd1 at the seedling and bolting stages. Genetic analysis showed that two recessive genes, designated BnChd1-1 and BnChd1-2, are responsible for the light-green phenotype. BnChd1-1 was determined to be a single Mendelian factor in a BC2F1 population based on a phenotypic segregation ratio of 1:1. BnChd1-1 was mapped to a region of A01 using a BC3F1 population of 394 individuals with 198 green and 196 light-green plants. Within the collinear region in Brassica rapa, six genes that might be involved in chloroplast thylakoid development and NDH dehydrogenase activity were annotated. Among the six candidate genes, reverse transcription-polymerase chain reaction revealed that the mRNA levels of Bra021529 and Bra040517 were undetectable in the mutant and high in Qingyou10 and Westar plants at the seedling stage. Additionally, DNA sequence differences were identified across the gene and promoter region. Protein sequence differences were also observed in Bra040517, while no sequence differences in Bra021529 were observed between Bnchd1 and Qingyou10. Therefore, the homologue of Bra040517 is the most likely candidate gene for BnChd1-1.

A simple genetic basis for complex social behaviour mediates widespread gene expression differences

A remarkable social polymorphism is controlled by a single Mendelian factor in the fire ant Solenopsis invicta. A genomic element marked by the gene Gp-9 determines whether workers tolerate one or many fertile queens in their colony. Gp-9 was recently shown to be part of a supergene with two nonrecombining variants, SB and Sb. SB/SB and SB/Sb queens differ in how they initiate new colonies, and in many physiological traits, for example odour and maturation rate. To understand how a single genetic element can affect all these traits, we used a microarray to compare gene expression patterns between SB/SB and SB/Sb queens of three different age classes: 1-day-old unmated queens, 11-day-old unmated queens and mated, fully reproductive queens collected from mature field colonies. The number of genes that were differentially expressed between SB/SB and SB/Sb queens of the same age class was smallest in 1-day-old queens, maximal in 11-day-old queens and intermediate in reproductive queens. Gene ontology analysis showed that SB/SB queens upregulate reproductive genes faster than SB/Sb queens. For all age classes, genes inside the supergene were overrepresented among the differentially expressed genes. Consistent with the hypothesized greater number of transposons in the Sb supergene, 13 transposon genes were upregulated in SB/Sb queens. Viral genes were also upregulated in SB/Sb mature queens, consistent with the known greater parasite load in colonies headed by SB/Sb queens compared with colonies headed by SB/SB queens. Eighteen differentially expressed genes between reproductive queens were involved in chemical signalling. Our results suggest that many genes in the supergene are involved in regulating social organization and queen phenotypes in fire ants.

A social rearrangement

Some worker fire ants will tolerate multiple queens in their colony, but others only one. It turns out that this behaviour is governed by a gene cluster on an unusual pair of chromosomes. Two scientists describe what these findings mean to the fields of social evolution, genetics and beyond. See Letter p.664 The fire ant Solenopsis invicta can be found living in two very different types of colony: in some the workers tolerate multiple queens yet in others they tolerate just one. This divergence is in the genes, under the control of a single Mendelian factor. This study presents a large-scale analysis of the genomic region involved and, surprisingly, the various aspects of this polymorphism are found to be governed by a non-recombining supergene occupying half a chromosome. The operation of this region is remarkably similar to that of sex chromosomes. These findings demonstrate how limiting local genetic rearrangements can maintain divergent social behaviours that involve many genes acting together.

Identification and mapping of a major dominant quantitative trait locus controlling seeds per silique as a single Mendelian factor in Brassica napus L.

One putative quantitative trait locus (QTL) for seeds per silique (SS), cqSS.A8, was identified using a double haploid (DH) population in Brassica napus, and near-isogenic lines (NILs; BC(3)F(1)) for cqSS.A8 were developed. However, the flanking markers from cqSS.A8 showed no significant difference using single-marker analysis, even though the frequency distribution of SS in the BC(3)F(1) was bimodal, suggesting that one novel locus existed. In this study, we characterized the effects of this locus in the NILs and used a published linkage map to determine its location. A three-step approach was designed for mapping the locus in the NILs (BC(3)F(2)): (1) determining the individual BC(3)F(2) genotype at the locus using a progeny test; (2) identifying amplified fragment length polymorphism (AFLP) markers linked to the locus using a combination of AFLP and bulked segregant analysis; and (3) determining the location and effects of this locus. QTL analysis in the BC(3)F(2) revealed that this locus explained 85.8 and 55.7 % of phenotypic variance for SS and SL, respectively. Its additive and dominant effects on SS were 6.1 and 5.7, respectively. The locus was validated using a DH population by composite interval mapping and located to linkage group C9 (designated as qSS.C9). Mapping qSS.C9 was undertaken using 230 extremely low-SS plants of a BC(4)F(1) population containing 807 plants. We found that qSS.C9 delimited a 1.005-Mb interval including 218 predicted genes in the reference Brassica rapa (Chiifu-401). These results will greatly facilitate map-based cloning of qSS.C9 and seed yield improvement in rapeseed.

Molecular Mapping of Sterility QTLs qSS-3, qSS-6a and qSS-7 as Single Mendelian Factors via NIL strategy

Hybrid sterility between Oryza glaberrima and O. sativa seriously hampers the introgression of favorable genes from each other. In order to further understand this issue, identification and isolation of hybrid sterility QTLs as single Mendelian factors are an effective strategy. A genetic map was constructed using a BC 1F 1 population derived from a cross between an O. sativa japonica cultivar and an O. glaberrima accession. Four main-effect QTLs for pollen sterility were detected in the BC 1F 1. Five BC 8F 1 advanced backcross populations were developed via successive backcrosses based on phenotype and molecular selections. The BC 8F 1 populations showed bimodal distribution for pollen fertility and could be classified into semi-sterile and fertile types, fitting single Mendilian factor inheritance ratios. Three QTLs detected in the BC 1F 1 corresponding to qSS-3, qSS-6a and qSS-7 were mapped on chromosomes 6, 3 and 7, respectively, as single Mendilian factors.

Characterization and precise mapping of a QTL increasing spike number with pleiotropic effects in wheat

Tiller number (TN) and spike number per plant (SN) are key components of grain yield and/or biomass in wheat. In this study, an introgression line 05210, developed by introgression of chromosomal segments from a synthetic exotic wheat Am3 into an elite cultivar Laizhou953, showed a significantly increased TN and SN, but shorter spike length (SL) and fewer grain number per spike (GNS) than Laizhou953. To investigate the quantitative trait locus (QTL) responsible for these variations, the introgressed segments in 05210 were screened by SSR markers and one follow-up segregation population was developed from the cross 05210/Laizhou953. The population showed 3:1 segregation ratios for SN, SL and GNS, indicating that QTLs for these traits have been dissected into single Mendelian factors. Bulked segregation analysis showed that the markers located on the 4B introgressed segment were polymorphic between the two bulks. Therefore, they were further analyzed in the F(2) population to construct a linkage map. Three new QTLs, QSn.sdau-4B, QSl.sdau-4B and QGns.sdau-4B, were detected for SN, SL and GNS, respectively, which explained a large portion of the phenotypic variation (30.1-67.6%) for these traits with overlapping peaks. Correlation analysis and multiple-trait, multiple-interval mapping (MMIM) suggested pleiotropic effects of the QTL on SN, SL and GNS. Therefore, the QTL was designated as QSn.sdau-4B. By a progeny test based on F(3) families using SN, the QTL was mapped as a Mendelian factor to the proximal region of 4BL. It is a key QTL responsible for variation in spike number and size, which had not been reported previously. Thus, it is an important QTL for wheat to achieve high and stable biomass and grain yield. Dissection and mapping of this QTL as a Mendelian factor laid a solid foundation for map-based cloning of grain yield-related QTLs in wheat.