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Summary: Mustard yield per plant is severely restricted by the seed number per silique. The seed number per silique in the Brassica juncea trilocular mutant J163‐4 is significantly greater than that in normal bilocular plants. However, how the trilocular silique of J163‐4 is formed remains unclear. Here, we studied the gene structure and function of mc2 in B. juncea and Arabidopsis using comparative morphology and molecular genetic experiments. We found that mc2 is a CLV1 ortholog, BjA7.CLV1. The deletion of cis‐regulatory region in mc2 promoter, which affects Mc2 expression in carpel margin meristem (CMM), led to trilocular silique formation. The BjCLV1 sequence with its complete promoter containing the cis‐regulatory region can restore the Bjclv1 and clv1 mutant phenotypes in B. juncea and Arabidopsis, respectively. Additionally, this cis‐regulatory region had a collinear segment in the promoter of CLV1 homologous gene in most Brassicaceae species. Our results are consistent with the report that BjCLV1 represents a conserved pleiotropic role in shoot meristem and CMM development, which contains a cis‐regulatory sequence specifically expressed BjCLV1 in CMM in its promoter, and this cis‐regulatory region is conserved in Brassicaceae species. These results offer a reliable approach for fine‐tuning the traits of seed yield in Brassicaceae crops. [ABSTRACT FROM AUTHOR]

Abstract Background Sucrose is the primary photosynthesis product and the principal translocating form within higher plants. Sucrose transporters (SUC/SUT) play a critical role in phloem loading and unloading. Photoassimilate transport is a major limiting factor for seed yield. Our previous research demonstrated that SUT co-localizes with yield-related quantitative trait loci. This paper reports the isolation of BnA7.SUT1 alleles and their promoters and their association with yield-related traits. Results Two novel BnA7.SUT1 genes were isolated from B. napus lines 'Eagle' and 'S-1300' and designated as BnA7.SUT1.a and BnA7.SUT1.b, respectively. The BnA7.SUT1 protein exhibited typical SUT features and showed high amino acid homology with related species. Promoters of BnA7.SUT1.a and BnA7.SUT1.b were also isolated and classified as pBnA7.SUT1.a and pBnA7.SUT1.b, respectively. Four dominant sequence-characterized amplified region markers were developed to distinguish BnA7.SUT1.a and BnA7.SUT1.b. The two genes were estimated as alleles with two segregating populations (F2 and BC1) obtained by crossing '3715'×'3769'. BnA7.SUT1 was mapped to the A7 linkage group of the TN doubled haploid population. In silico analysis of 55 segmental BnA7.SUT1 alleles resulted three BnA7.SUT1 clusters: pBnA7.SUT1.a- BnA7.SUT1.a (type I), pBnA7.SUT1.b- BnA7.SUT1.a (type II), and pBnA7.SUT1.b- BnA7.SUT1.b (type III). Association analysis with a diverse panel of 55 rapeseed lines identified single nucleotide polymorphisms (SNPs) in promoter and coding domain sequences of BnA7.SUT1 that were significantly associated with one of three yield-related traits: number of effective first branches (EFB), siliques per plant (SP), and seed weight (n = 1000) (TSW) across all four environments examined. SNPs at other BnA7.SUT1 sites were also significantly associated with at least one of six yield-related traits: EFB, SP, number of seeds per silique, seed yield per plant, block yield, and TSW. Expression levels varied over various tissue/organs at the seed-filling stage, and BnA7.SUT1 expression positively correlated with EFB and TSW. Conclusions Sequence, mapping, association, and expression analyses collectively showed significant diversity between the two BnA7.SUT1 alleles, which control some of the phenotypic variation for branch number and seed weight in B. napus consistent with expression levels. The associations between allelic variation and yield-related traits may facilitate selection of better genotypes in breeding.

Summary: Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high‐quality genome assembly of a typical semi‐winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single‐molecule sequencing and chromosome conformation capture (Hi‐C) techniques. Most of the high‐confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR‐RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide‐binding leucine‐rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head‐to‐head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi‐winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits. [ABSTRACT FROM AUTHOR]

SUMMARY: Brassica napus is currently cultivated as an important ornamental crop in China. Flower color has attracted much attention in rapeseed genetics and breeding. Here, we characterize an orange‐flowered mutant of B. napus that exhibits an altered carotenoid profile in its petals. As revealed by map‐based cloning, the change in color from yellow to orange is attributed to the loss of BnaC09.ZEP (zeaxanthin epoxidase) and a 1695‐bp deletion in BnaA09.ZEP. HPLC analysis, genetic complementation and CRISPR/Cas9 experiments demonstrated that BnaA09.ZEP and BnaC09.ZEP have similar functions, and the abolishment of both genes led to a substantial increase in lutein content and a sharp decline in violaxanthin content in petals but not leaves. BnaA09.ZEP and BnaC09.ZEP are predominantly expressed in floral tissues, whereas their homologs, BnaA07.ZEP and BnaC07.ZEP, mainly function in leaves, indicating redundancy and tissue‐specific diversification of BnaZEP function. Transcriptome analysis in petals revealed differences in the expression of carotenoid and flavonoid biosynthesis‐related genes between the mutant and its complementary lines. Flavonoid profiles in the petals of complementary lines were greatly altered compared to the mutant, indicating potential cross‐talk between the regulatory networks underlying the carotenoid and flavonoid pathways. Additionally, our results indicate that there is functional compensation by BnaA07.ZEP and BnaC07.ZEP in the absence of BnaA09.ZEP and BnaC09.ZEP. Cloning and characterization of BnaZEPs provide insights into the molecular mechanisms underlying flower pigmentation in B. napus and would facilitate breeding of B. napus varieties with higher ornamental value. Significance Statement: Few studies have cloned petal‐pigmentation genes and revealed the molecular mechanism underlying carotenoid‐based variation in flower color. Cloning and characterization of BnaZEPs in the present study provide insights into the molecular mechanisms underlying flower pigmentation in B. napus and would facilitate breeding of B. napus varieties with higher ornamental value. [ABSTRACT FROM AUTHOR]