Identification of a major QTL and candidate gene for flowering time in industrial hemp via BSA-seq and fine mapping.

Identification and functional validation of the BcFPA, a candidate regulator of flowering time in pak choi

Flowering time is an essential complex quantitative agronomic trait in pak choi ( Brassica rapa ssp. chinensis ). It exerts decisive effects on crop yield, commercial quality and environmental adaptability throughout the whole cultivation cycle. Uncovering the key genes controlling flowering time is therefore critical for molecular genetic research and genetic improvement of pak choi. In the present work, we performed bulked segregant sequencing (BSA-seq) using an F 2 segregating population derived from a cross between late-flowering inbred line M1-006 and early-flowering line M2-001 to isolate and functionally characterize the flowering-related gene. Finally, a major-effect QTL governing flowering time was mapped to a 2.62 Mb genomic interval on chromosome A09, harboring a total of 440 annotated genes. Further gene function annotation pinpointed Brap0046500.1 (designated BcFPA ), an ortholog of the autonomous-pathway flowering regulator AtFPA from Arabidopsis thaliana , as the promising candidate gene within this target region, which was subsequently verified via polymorphic InDel molecular markers and genotype screening of F 2 individuals. Combined sequence comparison and functional assays demonstrated that a non-synonymous substitution in the coding region of BcFPA leads to delayed floral transition in pak choi. Consistently, transgenic complementation assays in Arabidopsis fpa-1 loss-of-function mutants verified that the wild-type BcFPA allele was sufficient to rescue the late-flowering phenotype and restore normal flowering. Moreover, overexpression of BcFPA in transgenic pak choi significantly accelerated flowering, further corroborating its positive regulatory role in floral initiation. This research systematically reveals the genetic mechanism responsible for natural flowering time variation in Brassica rapa. The identified BcFPA gene and its linked molecular markers can serve as important genetic resources for marker-assisted selective breeding, facilitating the breeding of new pak choi varieties with optimal flowering traits.

Genetic Dissection and Fine-Mapping of QTL for Salinity Tolerance at the Reproductive Stage on Chromosome 2 of Rice Variety Nona Bokra

Soil salinity is a major constraint limiting rice productivity, particularly at the reproductive stage. To elucidate the genetic basis of reproductive stage salinity tolerance, this study validated and fine-mapped quantitative trait loci (QTL) for yield-related traits using a salinity-tolerant line SL506, identified through screening of Nona Bokra–CSSLs in a Koshihikari background. In 2016, the F2 population derived from SL506/Koshihikari was evaluated under long-term salt stress; three QTLs associated with plant dry weight, panicle number, and grain weight were detected on chromosome 2. In 2023, validation analysis using F3 individuals confirmed the presence of these QTLs. Subsequent fine-mapping using F4 near-isogenic lines (NILs) delimited the QTL to a 1.7 Mb interval and high-resolution mapping using an F5 recombinant population progressively refined it to a 473 kb genomic region containing 69 annotated genes. Variant Effect Predictor analysis identified 15 deleterious nonsynonymous variants (SIFT < 0.05) in six candidate genes. Based on annotated gene functions, predicted variant effects, and their membership in stress-related gene families, OsPP2C24, OsFbox102, and OsWAK14 were suggested as the most promising candidate genes underlying qPDW2. These findings provide insights into the genetic basis of reproductive-stage salinity tolerance from valuable resources for the future improvement of salt tolerance and yield stability in rice.

Day-neutral flowering candidate genes identified by selection mapping in an upland cotton (Gossypium hirsutum L.) RIL population

The PAF1 complex is identified as a priority candidate for the control of day-neutral flowering in upland cotton and warrant further investigation as a potential source of markers for marker-assisted introgression of reduced photoperiod sensitivity.

Dissecting seed oil content QTL and integrating their genetic effects for genomic prediction in Brassica napus

This study bridges the gap between high-resolution genetic dissection and predictive breeding, providing a practical framework to accelerate oil yield improvement in rapeseed.

Mapping the genetic architecture of flowering and maturity in soybean [Glycine max (L.) Merr.] using multi-locus genome-wide association studies under Ethiopian conditions

Fine mapping and candidate gene analysis of qKnps-2A for kernel number per spike in wheat

Kernel number per spike (KNPS) is a crucial determinant of wheat yield. Previous studies identified qKnps-2A as a major stable QTL for KNPS on chromosome 2A using a recombinant inbred line (RIL) population derived from a cross between the semi-winter wheat cultivar Kenong 9204 and the winter wheat cultivar Jing 411. However, fine mapping and gene cloning of this locus have not been reported. Using InDel markers developed from parental genomic data, the near-isogenic line (NIL) pairs and 11 key recombinants were identified from residual heterozygous line-derived segregating populations, delimiting qKnps-2A to a 5.13 Mb interval (616.30–621.43 Mb) harboring 50 high-confidence genes. Integrated transcriptome sequencing, expression profiling across tissues and developmental stages, sequence comparison, and haplotype analysis identified TraesCS2A03G0902100 , encoding a zinc knuckle protein, as the most likely candidate gene. Near-isogenic line analysis revealed that the Kenong 9204 allele significantly increased spikelet number per spike (2.94%), floret number per spike (10.51%), and KNPS (14.37%), resulting in a 7.32% yield increase, alongside improvements in grain quality traits. Phytohormone analysis showed the Kenong 9204 allele was associated with elevated IAA and IAA/ABA ratios during early spike development and reduced ABA during late development, suggesting hormone-related physiological changes linked to improved grain set. Haplotype analysis of 314 global accessions showed that Hap-KN9204 was significantly associated with increased KNPS, grain compactness, grain setting, and grain width. This superior haplotype predominates in Asia, Europe, and North America, and is suggestive of positive selection during Chinese wheat breeding, increasing from 30.00% in landraces to 59.62% in modern cultivars. This study fine-mapped qKnps-2A and identified TraesCS2A03G0902100 as the most likely candidate gene, which was associated with altered phytohormone profiles during spike development, suggesting physiological changes linked to enhanced yield. The superior Hap-KN9204 haplotype appears to have been favored by positive selection in Chinese wheat breeding, establishing qKnps-2A as a valuable target for yield improvement.