Mapping of Ppd-B1, a Major Candidate Gene for Late Heading on Wild Emmer Chromosome Arm 2BS and Assessment of Its Interactions with Early Heading QTLs on 3AL

Wheat heading date is an important agronomic trait determining maturation time and yield. A set of common wheat (Triticum aestivum var. Chinese Spring; CS)-wild emmer (T. turgidum L. subsp. dicoccoides (TDIC)) chromosome arm substitution lines (CASLs) was used to identify and allocate QTLs conferring late or early spike emergence by examining heading date. Genetic loci accelerating heading were found on TDIC chromosome arms 3AL and 7BS, while loci delaying heading were located on 4AL and 2BS. To map QTLs conferring late heading on 2BS, F₂ populations derived from two cross combinations of CASL2BS × CS and CASL3AL × CASL2BS were developed and each planted at two times, constituting four F₂ mapping populations. Heading date varied continuously among individuals of these four populations, suggesting quantitative characteristics. A genetic map of 2BS, consisting of 23 SSR and one single-stranded conformation polymorphism (SSCP) marker(s), was constructed using these F₂ populations. This map spanned a genetic length of 53.2 cM with average marker density of 2.3 cM. The photoperiod-sensitivity gene Ppd-B1 was mapped to chromosome arm 2BS as a SSCP molecular marker, and was validated as tightly linked to a major QTL governing late heading of CASL2BS in all mapping populations. A significant dominance by additive effect of Ppd-B1 with the LUX gene located on 3AL was also detected. CS had more copies of Ppd-B1 than CASL2BS, implying that increased copy number could elevate the expression of Ppd-1 in CS, also increasing expression of LUX and FT genes and causing CS to have an earlier heading date than CASL2BS in long days.     

Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome

A heterogeneous collection of rice genotypes which included seven salt-tolerant rice lines, one salt-sensitive improved line, one wild rice (Oryza rufipogon) and one salt-tolerant wild rice relative (Porteresia coarctata) was screened with ten salt-tolerance-linked simple sequence repeat markers, of which nine were from the Saltol QTL mapped on rice 1st chromosome and the rest one from 8th chromosome, having high phenotypic variance for salt tolerance. Variation in molecular weight (in the form of base pairs) of the different amplified products using RM primers was used to find out the genetic relationship among the studied rice genotypes. Genomic DNA of the studied genotypes was also amplified with a reported allele mining primer for a salt-inducible gene (salT). The amplified products were sequenced and aligned to find out the closeness among the rice lines for the studied gene. Dendrogram derived from marker profiles showed partial similarity with salT gene-derived tree. Commonly, all the salt-tolerant lines were grouped into a single cluster, including IR36 (a salt-sensitive line) to which O. rufipogon (the wild rice) and P. coarctata (the wild rice relative) joined separately. The taxonomic identity and evolutionary relationship among the three groups (rice, wild rice and wild rice relative) were bioinformatically analysed using the nucleotide sequence of the studied salT gene.     

Putative Thinopyrum intermedium-derived stripe rust resistance gene Yr50 maps on wheat chromosome arm 4BL

Stripe rust-resistant wheat introgression line CH223 was developed by crossing the resistant partial amphiploid TAI7047 derived from Thinopyrum intermedium with susceptible cultivars. The resistance is effective against all the existing Chinese stripe rust races, including the most widely virulent and predominant pathotypes CYR32 and CYR33. Cytological analyses using GISH detected no chromosomal segments from Th. intermedium. It was presumed that the segment was too small to be detected. Normal bivalent pairing at meiosis in CH223 and its hybrids confirmed its stability. Genetic analysis of the F₁, F₂, F₃ and BC₁ populations from crosses of CH223 with susceptible lines indicated that resistance was controlled by a single dominant gene. The resistance gene was mapped using an F_2:3 population from Taichung 29/CH223. The gene was linked to five co-dominant genomic SSR markers, Xgwm540, Xbarc1096, Xwmc47, Xwmc310 and Xgpw7272, and flanked by Xbarc1096 and Xwmc47 at 8.0 and 7.2 cM, respectively. Using the Chinese Spring nulli-tetrasomic and ditelosomic lines, the polymorphic markers and the resistance gene were assigned to chromosome arm 4BL. As no permanently named stripe rust resistance genes had been assigned to chromosome 4BL, this new resistance gene is designated Yr50. The gene, together with the identified closely linked markers, could be used in marker-assisted selection to combine two or more resistance genes in a single genotype.     

Tagging of an Aegilops speltoides Derived Leaf Rust Resistance Gene Lr 28 with a Microsatellite Marker in Wheat

Leaf rust resistance gene Lr28 has been transferred form Aegilops speltoides into bread wheat on chromosome 4AL. To identify the molecular markers linked to Lr28 the available microsatellite markers for wheat chromosome arm 4AL were surveyed on near isogenic lines (NILs) of Triticum aestivum cultivars having Lr28 gene, other Lrgenes and susceptible cultivars. A null allele of Xgwm 160 marker was found to be associated with Lr28. Linkage between the marker and the Lr28 resistance gene was confirmed using F₂ mapping population of cross PBW343 and HD2329 + Lr28.     

Segregation analysis of heading traits in hexaploid wheat utilizing recombinant inbred lines

The purpose of this study was to analyze the genetic segregation of heading traits in wheat using recombinant inbred lines (RILs) of hexaploid wheat, derived from Triticum aestivum cv. Chinese Spring and T. spelta var. duhameliamum. The population was examined under controlled environmental conditions as well as in the field. This strategy differentiated the effect of three genetic factors (vernalization requirement, photoperiod sensitivity and narrow-sense earliness) and identified their interactions. Correlation analysis showed that photoperiod sensitivity and narrow-sense earliness are critical for heading time in the field. Single-marker analysis using 322 molecular markers segregating among RIL detected a total of 38 linked markers for each genetic factor and heading in the field. In interval analysis, two Vrn genes (Vrn-B1 and Vrn-D1) and Ppd-B1 were mapped on chromosomes 5B, 5D and 2B, respectively. It was noticed that Vrn-B1 on 5B from the spelt wheat conferred a strong-spring habit equivalent to the homologous Vrn-A1. Quantitative trait locus analysis also showed that Ppd-B1 was not detected under the short-day condition without vernalization treatment, and that there were two types of genes for photoperiod sensitivity, dependent on and independent of vernalization treatment.     

Fine-mapping and molecular marker development for <Emphasis Type="Italic">Pi56(t),</Emphasis> a NBS-LRR gene conferring broad-spectrum resistance to <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis> in rice

The major quantitative trait locus qBR9.1 confers broad-spectrum resistance to rice blast, and was mapped to a ~69.1 kb region on chromosome 9 that was inherited from resistant variety Sanhuangzhan No 2 (SHZ-2). Within this region, only one predicted disease resistance gene with nucleotide binding site and leucine-rich repeat (NBS-LRR) domains was found. Specific markers corresponding to this gene cosegregated with blast resistance in F₂ and F₃ populations derived from crosses of susceptible variety Texianzhan 13 (TXZ-13) to SHZ-2 and the resistant backcross line BC-10. We tentatively designate the gene as Pi56(t). Sequence analysis revealed that Pi56(t) encodes an NBS-LRR protein composed of 743 amino acids. Pi56(t) was highly induced by blast infection in resistant lines SHZ-2 and BC-10. The corresponding allele of Pi56(t) in the susceptible line TXZ-13 encodes a protein with an NBS domain but without LRR domain, and it was not induced by Magnaporthe oryzae infection. Three new cosegregating gene-specific markers, CRG4-1, CRG4-2 and CRG4-3, were developed. In addition, we evaluated polymorphism of the gene-based markers among popular varieties from national breeding programs in Asia and Africa. The presence of the CRG4-2 SHZ-2 allele cosegregated with a blast-resistant phenotype in two BC₂F₁ families of SHZ-2 crossed to recurrent parents IR64-Sub1 and Swarna-Sub1. CRG4-1 and CRG4-3 showed clear polymorphism among 19 varieties, suggesting that they can be used in marker-assisted breeding to combine Pi56(t) with other target genes in breeding lines.     

Detection and verification of quantitative trait loci for resistance to Fusarium ear rot in maize

Fusarium ear rot caused by Fusarium verticillioides is a prevalent disease in maize which can severely reduce grain yields and quality. Identification of stable quantitative trait loci (QTL) for resistance to Fusarium ear rot is a basic prerequisite for understanding the genetic mechanism of resistance and for the use of marker-assisted selection. In this study, two hundred and ten F _2:3 families were developed from a cross between resistant inbred line BT-1 and susceptible inbred line Xi502, and were genotyped with 178 simple sequence repeat markers. The resistance of each line was evaluated in two environments by artificial inoculation using the nail-punch method. The resistance QTL were detected using the composite interval mapping method. Three QTL were detected on chromosomes 4, 5 and 10. Of them, the QTL on chromosome 4 (bin 4.05/06) had the largest resistance to Fusarium ear rot, and could explain 17.95?% of the phenotypic variation. For further verification of the QTL effect, we developed near-isogenic lines (NILs) carrying the QTL region on chromosome 4 using parental line Xi502 as the recurrent parent. In the NIL background, this QTL can increase the resistance by 33.7?C35.2?% if the resistance region is homozygous, and by 17.8?C26.5?% if the resistance region contains the heterozygous allele. The stable and significant resistance effect of the QTL on chromosome 4 lays the foundation for further marker-assisted selection and map-based cloning in maize.     

Mapping QTLs for submergence tolerance in rice using a population fixed for <Emphasis Type="Italic">SUB1A</Emphasis> tolerant allele

Submergence is a widespread problem of rice production, especially in low-lying areas in South and Southeast Asia. Despite the success of Sub1 mega varieties, repeated instances of prolonged and severe flooding in stress-prone areas suggests that the SUB1 gene is no longer sufficient in those regions and requires improved varieties with increased tolerance. A study was conducted to identify quantitative trait loci (QTLs) associated with submergence tolerance using 115 F₇ recombinant inbred lines (RILs) derived from the cross of Ciherang-Sub1, a popular Indonesian cultivar carrying the SUB1 gene that has relatively higher tolerance to submergence compared to the performance of most other Sub1 lines and the submergence and stagnant flooding tolerant IR10F365. As the tolerant allele at SUB1A on chromosome 9 was fixed in this mapping population, additional QTLs responsible for submergence tolerance were expected to be revealed. Genotyping with an Infinium 6K SNP chip resulted in 469 polymorphic markers that were then used for QTL mapping. Phenotyping was performed under complete submergence with two replicates. A major QTL for submergence derived from Ciherang-Sub1, named qSUB8.1, was detected on chromosome 8 with a LOD score of 10.3 and phenotypic variance of 27.5%. Additionally, a smaller QTL, also derived from Ciherang-Sub1, was detected on chromosome 2 with a LOD score of 3.5 and phenotypic variance of 12.7%. There was no digenic interaction detected between these QTLs suggesting their independent action. The QTLs detected in this study can be used in marker-assisted selection to further improve the tolerance of other Sub1 varieties.     

Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars

Backcrossed inbred lines (BILs) and a set of reciprocal chromosome segment substitution lines (CSSLs) derived from crosses between japonica rice cultivars Nipponbare and Koshihikari were used to detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance. In the BILs, we detected one QTL on chromosome 3 and one QTL on chromosome 12. The QTL on the short arm of chromosome 3 accounted for 45.0% of the phenotypic variance and the Nipponbare allele of the QTL increased germination percentage by 21.3%. In the CSSLs, we detected seven QTLs, which were located on chromosomes 2, 3 (two), 5, 8 and 11 (two). All Nipponbare alleles of the QTLs were associated with an increased rate of germination. The major QTL for pre-harvest sprouting resistance on the short arm of chromosome 3 was localized to a 474-kbp region in the Nipponbare genome by the SSR markers RM14240 and RM14275 by using 11 substitution lines to replace the different short chromosome segments on chromosome 3. This QTL co-localized with the low-temperature germinability gene qLTG3-1. The level of germinability under low temperature strongly correlated with the level of pre-harvest sprouting resistance in the substitution lines. Sequence analyses revealed a novel functional allele of qLTG3-1 in Nipponbare and a loss-of-function allele in Koshihikari. The allelic difference in qLTG3-1 between Nipponbare and Koshihikari is likely to be associated with differences in both pre-harvest sprouting resistance and low-temperature germinability.     

Characterization of the Fusarium wilt resistance Fom-2 gene in melon

The melon gene Fom-2, which confers resistance to Fusarium oxysporum f.sp. melonis (Fom) races 0 and 1, has been previously characterized by map-based cloning, and it encodes a protein with a nucleotide binding site (NBS) and leucine-rich repeats (LRRs). Here, we used the primer Fom2-LRR₁₆₃₉ to clone and sequence a partial LRR region of the Fom-2 gene in 11 melon accessions resistant to Fusarium wilt from various geographic regions. Our work revealed that the structure of the partial LRR domain is highly conserved between eight of these resistant accessions and is similar to the resistant allele in the previously characterized PI-161375 line. Conversely, PI-124111 is a unique line that presents the same resistant allele that was previously described in the MR-1 line. The accession Cum-355 presents a protein that differs from that encoded by both the resistant lines PI-161375 and MR-1. This result suggests that Cum-355 has a new resistant allele of Fom-2 that determines the same specificity. Importantly, based on the sequence of the Fom-2 LRR domain, two sequence characterized amplified region (SCAR) markers, Fom2-R₄₀₈ and Fom2-S₃₄₂, were developed for Fom-2 resistant and susceptible alleles, respectively. These allele-specific PCR markers could be used as co-dominant markers when their primer pairs were combined in a multiplex PCR reaction. The specificity of these functional markers (FM) was validated on a set of 27 genotypes representing several melon types. These FM markers are expected to enhance the reliability and cost-effectiveness of marker-assisted selection for the Fom-2 gene in melon.     

Validation of <Emphasis Type="Italic">DGAT1</Emphasis>-<Emphasis Type="Italic">2</Emphasis> polymorphisms associated with oil content and development of functional markers for molecular breeding of high-oil maize

The gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1-2) is a key quantitative trait locus that controls oil content and oleic acid composition in maize kernels. Here we re-sequenced the DGAT1-2 region responsible for oil variation in a maize landrace set and in 155 inbred lines (35 high-oil and 120 normal lines). The high-oil DGAT1-2 allele was present in most Northern Flint and Southern Dent populations but was absent in five of eight Corn Belt Dent open-pollinated populations and in most of the earlier inbred lines. Loss of the high-oil DGAT1-2 allele possibly resulted from genetic drift in the early twentieth century when a few Corn Belt Dent populations were selected for the development of high-grain-yield inbred lines. Association analysis detected significant effects of two PCR-based functional markers (HO06 and DGAT04; developed based on DGAT1-2 polymorphisms) on kernel oil content and oleic acid composition using the 155 inbred lines. Zheng58 and Chang7-2, the parent inbred lines of elite hybrid Zhengdan958, were used to transfer the favorable allele from the high-oil line By804 using marker-assisted backcrossing with the two functional markers. In BC5F2:3 populations, oil content of the three genotypes (−/−, +/−, and +/+) was, respectively, 3.37, 4.20, and 4.61% (Zheng58 recipient line) and 4.14, 4.67, and 5.25% (Chang7-2 recipient line). Oil content of homozygous kernels containing the high-oil DGAT1-2 allele increased by 27–37% compared with recurrent parents. Hence, these functional markers can be used to re-introduce the high-oil DGAT1-2 allele into modern inbred lines for increased oil content through marker-assisted backcrossing.     

Mapping and characterization of the new adult plant leaf rust resistance gene <Emphasis Type="Italic">Lr77</Emphasis> derived from Santa Fe winter wheat

Key message

A new gene for adult plant leaf rust resistance in wheat was mapped to chromosome 3BL. This gene was designated as Lr77.

Abstract

‘Santa Fe’ is a hard red winter cultivar that has had long-lasting resistance to the leaf rust fungus, Puccinia triticina. The objective of this study was to determine the chromosome location of the adult plant leaf rust resistance in Santa Fe wheat. A partial backcross line of ‘Thatcher’ (Tc) wheat with adult plant leaf rust resistance derived from Santa Fe was crossed with Thatcher to develop a Thatcher//Tc*2/Santa Fe F₆ recombinant inbred line (RIL) population. The RIL population and parental lines were evaluated for segregation of leaf rust resistance in three field plot tests and in an adult plant greenhouse test. A genetic map of the RIL population was constructed using 90,000 single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. A significant quantitative trait locus for reduction of leaf rust severity in all four tests was found on chromosome 3BL that segregated as a single adult plant resistance gene. The RILs with the allele from the resistant parent for SNP marker IWB10344 had lower leaf rust severity and a moderately resistant to moderately susceptible response compared to the susceptible RILs and Thatcher. The gene derived from Santa Fe on chromosome 3BL was designated as Lr77. Kompetitive allele-specific polymerase chain reaction assay markers linked to Lr77 on 3BL should be useful for selection of wheat germplasm with this gene.

     

Mutant Alleles of Photoperiod-1 in Wheat (Triticum aestivum L.) That Confer a Late Flowering Phenotype in Long Days

Flowering time in wheat and barley is known to be modified by mutations in the Photoperiod-1 (Ppd-1) gene. Semi-dominant Ppd-1a mutations conferring an early flowering phenotype are well documented in wheat but gene sequencing has also identified candidate loss of function mutations for Ppd-A1 and Ppd-D1. By analogy to the recessive ppd-H1 mutation in barley, loss of function mutations in wheat are predicted to delay flowering under long day conditions. To test this experimentally, introgression lines were developed in the spring wheat variety ‘Paragon’. Plants lacking a Ppd-B1 gene were identified from a gamma irradiated ‘Paragon’ population. These were crossed with the other introgression lines to generate plants with candidate loss of function mutations on one, two or three genomes.Lines lacking Ppd-B1 flowered 10 to 15 days later than controls under long days. Candidate loss of function Ppd-A1 alleles delayed flowering by 1 to 5 days while candidate loss of function Ppd-D1 alleles did not affect flowering time. Loss of Ppd-A1 gave an enhanced effect, and loss of Ppd-D1 became detectable in lines where Ppd-B1 was absent, indicating effects may be buffered by functional Ppd-1 alleles on other genomes. Expression analysis revealed that delayed flowering was associated with reduced expression of the TaFT1 gene and increased expression of TaCO1.A survey of the GEDIFLUX wheat collection grown in the UK and North Western Europe between the 1940s and 1980s and the A.E. Watkins global collection of landraces from the 1920s and 1930s showed that the identified candidate loss of function mutations for Ppd-D1 were common and widespread, while the identified candidate Ppd-A1 loss of function mutation was rare in countries around the Mediterranean and in the Far East but was common in North Western Europe. This may reflect a possible benefit of the latter in northern locations.     

Mapping and genotypic analysis of the NK-lysin gene in chicken

Background

Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds.

Results

A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same {"type":"entrez-nucleotide","attrs":{"text":"NW_003779909","term_id":"358468969","term_text":"NW_003779909"}}NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines.

Conclusions

The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.     

Identification and mapping of a thermo-sensitive genic self-incompatibility gene in maize

In this study, we describe a novel ecological self-incompatibility (SI) line HE97 in maize. The main environmental factors influencing the inbred line characteristics were identified through field sowing trials during a two-year study period (2001 and 2002). The results showed that daily minimum temperature had the greatest effect on floral morphology and breeding system of the SI line. In staminate floret differentiation, when the daily minimum temperature exceeded 24°C, the line exhibited complete self-compatibility; however SI was observed when the daily minimum temperature was below 20°C. Therefore, we characterized the line as exhibiting thermo-sensitive genic self-incompatibility (TGSI). A set of F₂ and F_2:3 populations, derived from the inbred lines HE97 and Z58, were evaluated for two years to elucidate the TGSI line patterns of inheritance. Classical genetic analyses and QTL mapping results revealed that HE97 self-incompatibility was governed by a single allele, named here astgsi1. Thetgsi1 gene was mapped to chromosome 2 between SSR markers nc131 and bnlg1633, with a distance of 2.40 cM from nc131 and 2.44 cM from bnlg1633.     

Characterization of a wheat–Thinopyrum bessarabicum (T2JS-2BS·2BL) translocation line

Thinopyrum bessarabicum (2n = 2x = 14, JJ or E^bE^b) is an important genetic resource for wheat improvement due to its salinity tolerance and disease resistance. Development of wheat–Th. bessarabicum translocation lines will facilitate its practical utilization in wheat improvement. In this study, a novel wheat–Th. bessarabicum translocation line T2JS-2BS·2BL, which carries a segment of Th. bessarabicum chromosome arm 2JS was identified and further characterized using sequential chromosome C-banding, genomic in situ hybridization (GISH), dual-color fluorescent in situ hybridization (FISH) and DNA markers. The translocation breakpoint was mapped within bin C-2BS1-0.53 of chromosome 2B through marker analysis. Compared to the Chinese Spring (CS) parent and to CS-type lines, the translocation line has more fertile spikes per plant, longer spikes, more grains per spike and higher yield per plant, which suggests that the alien segment carries yield-related genes. However, plants with the translocation are also taller, head later and have lower 1,000-kernel weight than CS or CS-type lines. By using markers specific to the barley photoperiod response gene Ppd-H1, it was determined that the late heading date was conferred by a recessive allele located on the 2JS segment. In addition, four markers specific for the translocated segment were identified, which can be used for marker-aided screening.     

Genetic studies of self-fertility in rye (Secale cereale L.). 2. The search for isozyme marker genes linked to self-incompatibility loci

The segregation of several isozyme marker genes has been studied in F₂ inbred families from hybrids between self-sterile and five self-fertile inbred lines (nos. 2, 3, 4, 5, and 8) as well as from interline hybrids. Self-pollination of F₁ hybrids between self-sterile forms and lines 5 and 8 gave an F₂ segregation ratio of 1 heterozygote:1 homozygote for the gene Prx7 (chromosome 1R) against the allele from the line. This is interpreted as a result of tight linkage of the Prx7 gene with the S1 gene in chromosome 1R (recombination at a level of 0–1%). The self-pollination of such hybrids with lines 2,3 and 4 gave normal segregation for the Prx7 gene (1:2:1). This means that these lines carry a self-fertility allele which is not on chromosome 1R. Interline hybrids 5×2, 5×3 and 5×4 had self-fertility alleles for the two S genes and in inbred F₂ progenies gave the expected deviating segregation for the Prx7 gene in a ratio of 2:3:1. The segregation of interline hybrid 5×8 was normal, 1:2:1, as expected. Highly-deviating segregation in an inbred F₂ family of a hybrid with line 5 has also been obtained for another gene from chromosome 1R — Pgi2 (recombination with the S1 locus of 16.7%). By using the same method it has been estimated that line 4 has a self-fertility allele of the S2 locus from chromosome 2R and that the genes -Glu and Est4/11 are linked with it (recombination 16.7% and 17.5–20% respectively). Lines 2 and 3 have a self-fertility allele of the S5 locus from chromosome 5R which is linked with the Est5-7 gene complex (recombination at a level of 28.8–36.0%).     

A major QTL (<Emphasis Type="Italic">qFT12.1</Emphasis>) allele from wild soybean delays flowering time

Soybean is highly sensitive to photoperiod. To improve the adaptability and productivity of soybean, it is essential to understand the molecular mechanisms regulating flowering time. To identify new flowering time QTLs, we evaluated a BC₃F₅ population consisting of 120 chromosome segment substitution lines (CSSLs) over 2 years under field conditions. CSSLs were derived from a cross between the cultivated soybean cultivar Jackson and the wild soybean accession JWS156-1, followed by continuous backcrossing using Jackson as the recurrent parent. Four QTLs (qFT07.1, qFT12.1, qFT12.2, and qFT19.1) were detected on three chromosomes. Of these, qFT12.1 showed the highest effect, accounting for 36.37–38.27% of the total phenotypic variation over 2 years. This QTL was further confirmed in the F₇ recombinant inbred line population (n?=?94) derived from the same cross (Jackson × JWS156-1). Analysis of the qFT12.1 BC₃F₅ residual heterozygous line RHL509 validated the allele effect of qFT12.1 and revealed that the recessive allele of qFT12.1 resulted in delayed flowering. Evaluating the qFT12.1 near-isogenic lines (NILs) under different growth conditions showed that NILs with the wild soybean genotype always showed later flowering than those with the cultivated soybean genotype. qFT12.1 was delimited to a 2703-kb interval between the markers BARCSOYSSR_12_0220 and BARCSOYSSR_12_0368 on chromosome 12. qFT12.1 may be a new flowering time gene locus in soybean.