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Key message: The QTLs and candidate genes governing the multifoliolate phenotype were identified by combining linkage mapping with BSR-seq, revealing a possible interplay between genetics and the environment in soybean leaf development. Soybean, as a legume, is typified by trifoliolate leaves. Although multifoliolate leaves (compound leaves with more than three leaflets each) have been reported in soybean, including sporadic appearances in the first compound leaves in a recombinant inbred line (RIL) population from a cross between cultivated soybean C08 and wild soybean W05 from this study, the genetic basis of this phenomenon is still unclear. Here, we integrated quantitative trait locus (QTL) mapping with bulked segregant RNA sequencing (BSR-seq) to identify the genetic loci associated with the multifoliolate phenotype in soybean. Using linkage mapping, ten QTLs related to the multifoliolate trait were identified. Among these, a significant and major QTL, qMF-2-1 on chromosome 2 and consistently detected across biological replicates, explained more than 10% of the phenotypic variation. Together with BSR-seq analyses, which analyzed the RILs with the highest multifoliolate frequencies and those with the lowest frequencies as two distinct bulks, two candidate genes were identified: Glyma.06G204300 encoding the transcription factor TCP5, and Glyma.06G204400 encoding LONGIFOLIA 2 (LNG2). Transcriptome analyses revealed that stress-responsive genes were significantly differentially expressed between high-multifoliolate occurrence lines and low occurrence ones, indicating environmental factors probably influence the appearance of multifoliolate leaves in soybean through stress-responsive genes. Hence, this study offers new insights into the genetic mechanism behind the multifoliolate phenotype in soybean. [ABSTRACT FROM AUTHOR]

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease, leading to huge yield losses in wheat production. Identification of resistance genes and closely linked molecular markers can greatly facilitate breeding resistant wheat cultivars. Shaannong69 conferred high resistance to stripe rust both at the seedling and adult-plant stages. The Pst race CYR31 was used to infect Shaannong69, Huixianhong, F1 and F2 plants and F2:3 lines at the seedling stage in the greenhouse. Genetic analysis identified a single dominant gene, designated as YrSN69, conferring resistance to Pst race CYR31 in Shaannong69. Seventy-four of 176 SNPs with the absolute value of ∆SNP-index more than 0.85 were identified in 753.33–766.18 Mb on chromosome 2BL based on bulked segregant RNA sequencing. Fifteen kompetitive allele-specific PCR markers were developed to genotype susceptible F2 plants derived from the Shaannong69/Huixianhong cross. YrSN69 was mapped on chromosome arm 2BL in a 2.0 cM genetic interval, with genetic distances of 0.2 cM and 1.8 cM to markers 2BC17 and 2BA20, respectively, corresponding to a 3.16 Mb physical region based on the IWGSC RefSeq v1.1 with 44 high-confidence annotated genes. The YrSN69 is likely to be a new allele of Yr72 in comparison with known Yr genes on chromosome 2BL. These results provide a solid foundation for map-based cloning of YrSN69 and marker-assisted selection for pyramiding stripe rust resistance genes. [ABSTRACT FROM AUTHOR]

Genic male sterility (GMS) is a common and important trait, which is widely used for the production of hybrid seeds. However, the molecular mechanism of GMS in watermelon remains poorly understood. In this study, we comparatively analyzed the transcriptome profiles of sterile and fertile floral buds using the bulked segregant analysis (BSA) and transcriptome sequencing (RNA-seq). A total of 2507 differentially expressed genes (DEGs) including 593 up-regulated and 1914 down-regulated, were identified to be related to male sterility in watermelon line Se18. Gene ontology (GO) analysis showed that 57 GO terms were significantly enriched, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed plant hormone signal transduction, glycolysis/gluconeogenesis, starch and sucrose metabolism, plant–pathogen interaction, phenylpropanoid biosynthesis pathways were obviously enriched. Furthermore, the efficiency of the RNA-seq analysis was validated by quantitative real-time PCR (qRT-PCR). Among the DEGs, some valuable candidate genes involved in pollen development were identified, such as gene Cla000029, a bHLH transcription factor and homologous to MS1 in Arabidopsis. Moreover, other DEGs including MYB gene Cla012590 (MYB26), Cla017100 (MYB21), etc., also provide useful information for further understanding the function of key genes involved in pollen development. This study provides new insights into the global network of male sterility in watermelon. [ABSTRACT FROM AUTHOR]

Leaf morphology varies significantly among Brassica juncea. However, little is known regarding the causal gene that controls lobed leaf shape in B. juncea. In our study, the BjRCO gene, which is associated with leaf morphological variation, was cloned from chromosome A10 in B. juncea via BSR-seq. Blast analysis suggested that the BjRCO encodes a HD-Zip I transcription factor, which may serve as a positive regulator of lobed leaf formation in leaf mustard. Interestingly, the lobed leaf genes reported in the related species of Brassica (B. rapa, B. napus, and B. juncea) were located in A10. Phylogenetic analysis showed that BjRCO was also homologous to the lobed leaf gene BoLl reported on chromosome 9 in B. oleracea. In addition, qRT-PCR results showed that the expression levels of the BjRCO gene were higher expressed in the inner small lobed leaves than in the little sawtooth-like leaves (LSL). These results of this study indicate that the BjRCO gene is related to lobed leaf formation in B. juncea. These findings help to establish a solid foundation for future research investigating the molecular mechanism governing lobed leaf formation in B. juncea. [ABSTRACT FROM AUTHOR]

Identification of the source of genetic variation in the large and complex genome of sugarcane has been comparatively less explored through next-generation sequencing tools. In this study, RNA-seq libraries of two extreme bulks from a segregating full-sib population and its parents were used to identify highly significant, alternate splicing (AS) events and premature stop codons (PMC) associated with early sucrose accumulation. An important differential AS event was identified within the β-subunit of pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP) which plays a key role in carbon partitioning in sugarcane. Premature stop codons that could result in truncated proteins were also detected in genes coding for aquaporin, aldolase, cytochrome C-oxidase, ribophorin and plant plasma membrane intrinsic proteins. A major proportion of these AS events and premature stop codons was validated for their differential enrichment in an independent set of sugarcane varieties having high and low sucrose content. The results provide useful insights into the role of putative AS events and premature stop codons which could be useful as candidate markers in marker-assisted breeding for developing high sugar varieties in sugarcane. [ABSTRACT FROM AUTHOR]

Abundant anthocyanins accumulate in many flowers, leaves, fruits, as well as stems. In this study, an F segregating population derived from a cross between Chinese kale with a purple stem and kale with a green stem was used to decipher the genetic basis for the stem color. Bulked segregant analysis in combination with RNA sequencing (BSR-seq) was used to genetically map the causal gene for the purple stem ( Ps), and the allele frequency difference between the two pools showed a single peak on chromosome C09. Ps was fine-mapped to the 0.32 cM interval with 406 kb sequences. A gene-encoding dihydroflavonol 4-reductase ( DFR), an enzyme in the anthocyanin biosynthesis pathway, was differentially expressed between the two pools, and was identified as the candidate gene for the purple stem in Chinese kale. Sequence analysis revealed that 1 bp was inserted in the coding sequence of exon 2 of the BoDRF gene in green kale, causing frameshift and loss of function. The expression level of the BoDFR gene was significantly lower than the Chinese kale cultivar with a purple stem. The genetic results of the Ps gene will be useful for future development of purple vegetables. [ABSTRACT FROM AUTHOR]