Molecular Breeding最新文献

The tassel competes with the ear for nutrients and shields the upper leaves, thereby reducing the yield of grain. The tassel branch number (TBN) is a pivotal determinant of tassel size, wherein the reduced TBN has the potential to enhance the transmission of light and reduce the consumption of nutrients, which should ultimately result in increased yield. Consequently, the TBN has emerged as a vital target trait in contemporary breeding programs that focus on compact maize varieties. In this study, QTL-seq technology and advanced population mapping were used to rapidly identify and dissect the major effects of the TBN on QTL. Advanced mapping populations (BC₄F₂ and BC₄F₃) were derived from the inbred lines 18-599 (8-11 TBN) and 3237 (0-1 TBN) through phenotypic recurrent selection. First, 13 genomic regions associated with the TBN were detected using quantitative trait locus (QTL)-seq and were located on chromosomes 2 and 5. Subsequently, validated loci within these regions were identified by QTL-seq. Three QTLs for TBN were identified in the BC₄F₂ populations by traditional QTL mapping, with each QTL explaining the phenotypic variation of 6.13-18.17%. In addition, for the major QTL (qTBN2-2 and qTBN5-1), residual heterozygous lines (RHLs) were developed from the BC₄F₂ population. These two major QTLs were verified in the RHLs by QTL mapping, with the phenotypic variation explained (PVE) of 21.57% and 30.75%, respectively. Near-isogenic lines (NILs) of qTBN2-2 and qTBN5-1 were constructed. There were significant differences between the NILs in TBN. These results will enhance our understanding of the genetic basis of TBN and provide a solid foundation for the fine-mapping of TBN.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01431-y.

The grain protein content is an important quality trait in cereals, and the expression level of the OsAAP6 can significantly affect the grain protein content in rice. Through site-directed mutagenesis, we found that the position from -7 to -12 bp upstream of the transcription start site of the OsAAP6 was the functional variation site. By using the yeast single hybrid test, point-to-point in yeast, and the local surface plasmon resonance test, the OsNAC74 was screened and verified to be a regulator upstream of OsAAP6. The OsNAC74 is a constitutively expressed gene whose product is located on the cell membrane. The OsAAP6 and the genes related to the seed storage in the Osnac74 mutants were downregulated, and grain protein content was significantly reduced. In addition, OsNAC74 had a significant impact on quality traits such as grain chalkiness and gel consistency in rice. Although the Osnac74 mutant seeds were relatively small, the individual plant yield was not decreased. Therefore, OsNAC74 is an important regulatory factor with multiple biological functions. This study provides important information for the later use of OsNAC74 gene for molecular design and breeding in rice.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01433-w.

Olive is an ancient oil-producing tree, widely cultivated in Mediterranean countries, and now spread to other areas of the world, including China. Recently, several molecular databases were constructed in different countries and platforms for olive identification using simple sequence repeats (SSRs) or single-nucleotide polymorphisms (SNPs). However, comparing their results across laboratories was difficult. Herein, hundreds of polymorphic single-copy nuclear sequence markers were developed from the olive genome. Using the advantage of multiplex PCR amplification and high-throughput sequencing, a fingerprint database was constructed for the majority of olives cultivated in China. We used 100 high-quality sequence loci and estimated the genetic diversity and structure among all these varieties. We found that compared with that based on SSRs, the constructed fingerprint database based on these 100 sequences or a few of them, could provide a reliable olive variety identification platform in China, with high discrimination among different varieties using the principle of BLAST algorithm. An example of such identification platform based on this study was displayed on the web for the olive database in China (http://olivedb.cn/jianding). After resolving redundant genotypes, we identified 126 olive varieties with distinct genotypes in China. These varieties could be divided into two clusters, and it was revealed that the grouping of the varieties has a certain relationship with their origin. Herein, it is concluded that these single-copy orthologous nuclear sequences could be used to construct a universal fingerprint database of olives across different laboratories and platforms inexpensively. Based on such a database, variety identification can be performed easily by any laboratory, which would further facilitate olive breeding and variety exchange globally.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01434-9.

Suitable flowering time can improve fiber yield and quality, which is of great significance for jute biological breeding. In this study, 242 jute accessions were planted in Fujian for 2 consecutive years, and 244,593 SNPs distributed in jute genome were used for genome-wide association analysis of flowering time. A total of 19 candidate intervals (P < 0.0001) were identified by using GLM and FaST-LMM and were significantly associated with flowering time, with phenotypic variation explained (PVE) ranging from 5.8 to 18.61%. Six stable intervals that were repeatedly detected in different environments were further identified by the linkage disequilibrium heatmap. The most likely 7 candidate genes involved to flowering time were further predicted according to the gene functional annotations. Notably, functional analysis of the candidate gene CcPRR7 of the major loci qFT-3-1, a key factor in circadian rhythm in the photoperiodic pathway, was evaluated by linkage, haplotype, and transgenic analysis. β-glucuronidase (GUS) and luciferase (LUC) activity assay of the promoters with two specific haplotypes confirmed that the flowering time can be controlled by regulating the expression of CcPRR7. The model of CcPRR7 involved in the photoperiod regulation pathway under different photoperiods was proposed. These findings provide insights into genetic loci and genes for molecular marker-assisted selection in jute and valuable information for genetically engineering PRR7 homologs in plants.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01435-8.

Low temperature and cold damage are natural factors that seriously reduce wheat yield. Thus, how to improve the cold resistance of wheat has been the focus of wheat breeders and geneticists. However, the genetic improvement for this trait has been slow, mainly because cold resistance is a complex quantitative trait and field phenotypic identification is relatively difficult. Therefore, the discovery, mapping, and cloning of the cold resistance genes of wheat provide a theoretical basis for the genetic improvement of wheat against cold resistance and facilitate the analysis of the molecular mechanisms of cold resistance in wheat. This study used the wheat line H261 and its EMS mutants LF2099 and XiNong 239 as materials. Cold trait segregation occurred in the F₂ generation of mutants LF2099 and XiNong 239 at a 15:1 separation ratio. Genetic analysis showed that two dominant overlapping genes, temporarily named Wcr-3 and Wcr-4, control cold resistance in wheat. Furthermore, a combined BSA and SNP array established that Wcr-3 is between BU100519 (SSR marker) and AX-94843669 (SNP marker). The markers are 1.32 cM apart, corresponding to the 5.41 Mb physical interval on the Chinese Spring 2B chromosome with 67 functionally annotated genes. Wcr-4 is located between AX-94657955 (SNP marker) and LC-23 (SSR marker), which are 1.79 cM apart, corresponding to a 2.35 Mb physical interval on the Chinese Spring 2D chromosome, which contains 66 functionally annotated genes. Wcr-3 and Wcr-4 are two new cold resistance genes, laying the foundation for their fine mapping and cloning.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01425-w.

Accurately identifying varieties with targeted agronomic traits was thought to contribute to genetic selection and accelerate rice breeding progress. Genomic selection (GS) is a promising technique that uses markers covering the whole genome to predict the genomic-estimated breeding values (GEBV), with the ability to select before phenotypes are measured. To choose the appropriate GS models for breeding work, we analyzed the predictability of nine agronomic traits measured from a population of 459 diverse rice varieties. By the comparison of eight representative GS models, we found that the prediction accuracies ranged from 0.407 to 0.896, with reproducing kernel Hilbert space (RKHS) having the highest predictive ability in most traits. Further results demonstrated the predictivity of GS is altered by several factors. Moreover, we assessed the method of integrating genome-wide association study (GWAS) into various GS models. The predictabilities of GS combined peak-associated markers generated from six different GWAS models were significantly different; a recommendation of Mixed Linear Model (MLM)-RKHS was given for the GWAS-GS-integrated prediction. Finally, based on the above result, we experimented with applying the P-values obtained from optimal GWAS models into ridge regression best linear unbiased prediction (rrBLUP), which benefited the low predictive traits in rice.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01423-y.

Chlorophyll is one of the key factors for photosynthesis and plays an important role in plant growth and development. We previously isolated an EMS mutagenized rapeseed chlorophyll-reduced mutant (crm1), which had yellow leaf, reduced chlorophyll content and fewer thylakoid stacks. Here, we found that crm1 showed attenuated utilization efficiency of both light energy and CO₂ but enhanced heat dissipation efficiency and greater tolerance to high-light intensity. BSA-Seq analysis identified a single nucleotide change (C to T) and (G to A) in the third exon of the BnaA01G0094500ZS and BnaC01G0116100ZS, respectively. These two genes encode the magnesium chelatase subunit I 1 (CHLI1) that catalyzes the insertion of magnesium into protoporphyrin IX, a pivotal step in chlorophyll synthesis. The mutation sites resulted in an amino acid substitution P144S and G128E within the AAA+ domain of the CHLI1 protein. Two KASP markers were developed and co-segregated with the yellow leaf phenotype in segregating F₂ population. Loss of BnaA01.CHLI1 and BnaC01.CHLI1 by CRISPR/Cas9 gene editing recapitulated the mutant phenotype. BnaA01.CHLI1 and BnaC01.CHLI1 were located in chloroplast and highly expressed in the leaves. Furthermore, RNA-seq analyses revealed the expression of chlorophyll synthesis-related genes were upregulated in the crm1 mutant. These findings provide a new insight into the regulatory mechanism of chlorophyll synthesis in rapeseed and suggest a novel target for improving the photosynthetic efficiency and tolerance to high-light intensity in crops.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01429-6.

Seed weight, which is highly correlated to seed size, is a critical agronomic trait that determines the yield of Brassica napus. However, there have been limited researches on the genes involved in regulating seed size. In Arabidopsis thaliana, ENHANCER OF DA1 (EOD1), an E3 ubiquitin ligase gene, has been identified as a significant negative regulator in controlling organ size, but the function of its homologs in rapeseed remains unknown. Only two homologous of EOD1, BnaEOD1.A04 and BnaEOD1.C04, have been found in B. napus and were mutated using the CRISPR-Cas9 system. Three T-DNA-free lines, T₂-157-1-C8, T₂-390-2-B8, and T₂-397-2-E2, were identified from the homozygous T₂ mutant lines. The BnaEOD1.A04 showed a similar type of editing in these mutants, whereas the BnaEOD1.C04 in T₂-397-2-E2 was only missing 26 amino acids, and the translation was not prematurely terminated, which was different from the other two mutants. In parallel, mutation of BnaEOD1s resulted in a noteworthy increase in both seed size and seed weight in the three editing lines. Additionally, there was a significant decline in the number of seeds per silique (SPS) and silique length (SL) in T₂-157-1-C8 and T₂-390-2-B8, but T₂-397-2-E2 did not show any significant changes in the SPS and SL, possibly due to distinct types of editing in the three lines. The above results indicate the conserved function of EOD1 homologs and provides promising germplasm for breeding novel high-yield rapeseed varieties by improving seed size and thousand-seed weight.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01430-z.

Ear traits are key contributors to grain yield in maize; therefore, exploring their genetic basis facilitates the improvement of grain yield. However, the underlying molecular mechanisms of ear traits remain obscure in both inbred lines and hybrids. Here, two association panels, respectively, comprising 203 inbred lines (IP) and 246 F₁ hybrids (HP) were employed to identify candidate genes for six ear traits. The IP showed higher phenotypic variation and lower phenotypic mean than the HP for all traits, except ear tip-barrenness length. By conducting a genome-wide association study (GWAS) across multiple environments, 101 and 228 significant single-nucleotide polymorphisms (SNPs) associated with six ear traits were identified in the IP and HP, respectively. Of these significant SNPs identified in the HP, most showed complete-incomplete dominance and over-dominance effects for each ear trait. Combining a gene co-expression network with GWAS results, 186 and 440 candidate genes were predicted in the IP and HP, respectively, including known ear development genes ids1 and sid1. Of these, nine candidate genes were detected in both populations and expressed in maize ear and spikelet tissues. Furthermore, two key shared genes (GRMZM2G143330 and GRMZM2G171139) in both populations were found to be significantly associated with ear traits in the maize Goodman diversity panel with high-density variations. These findings advance our knowledge of the genetic architecture of ear traits between inbred lines and hybrids and provide a valuable resource for the genetic improvement of ear traits in maize.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01426-9.