Genome resequencing reveals the evolutionary history of garlic reproduction traits.

"data availability statement the reported variation data from whole-genome sequencing have been deposited in the genome variation map (gvm) in the big data center beijing institute of genomics (big) chinese academy of science under the project accession numbers prjca006629 and prjca012274. bolting and non-bolting genotypes differed in performance ( supplementary data s1 ).; our assessment of the bolting ability of the studied genotypes showed that bolting ratios varied among the five groups ( supplementary data s2 ).; a total of 3539 genes showed a change in expression in reproductive stage garlic leaves compared with vegetative growth ( supplementary data s3 ; supplementary data table s9 ).; of these genes94 116 63 and 47 underwent potential selection in cg1 cg2 g3 and g4 respectively and 38 showed significant selective signals in at least two garlic groups ( supplementary data s4 ).; these genes constitute a putative regulatory network for controlling garlic bolting ( supplementary data s5 ).; of these 34 degs seven were co -like genes and six were ft -homolog genes ( supplementary data s6 and s7 ).; we found that the overexpression of these genes caused early flowering in transgenic arabidopsis ( supplementary data s8 ).; notably the co -like asa3g00698 1 and flowering-promoting ft -like asa6g06199 1 [ ] were selected in cg1 and g3 respectively during garlic evolution/domestication ( fig 3a supplementary data s9 ).; we also identified a b-box zinc finger protein (bbx)-encoding asa2g00291 1 with a distinct selection signature in both cg1 and g4 ( supplementary data s9 ).; only one haplotype could be identified in this group ( supplementary data s10 ).; asa5g01527 1 encodes a putative global transcription factor group e (gte) protein which is an ortholog of arabidopsis gte10 ( supplementary data s11 ).; the number of cells in each cluster ranged from 19 to 1885 and the number of expressed genes ranged from 8229 to 26 347 ( supplementary data s12 ).; investigation of cluster-specific genes indicated that cells of cluster 3 (c3; 'cluster' is abbreviated as 'c' hereafter) and c4 were xylem-type whereas those of c5 c6 c8 and c9 were stem cells epidermis sieve and proliferative cells respectively ( fig 5c and d supplementary data s13 ).; these cell identities were further verified by functional enrichment of the cluster-active genes ( supplementary data s14 - s19 ).; developmental trajectories of basal plate-cells indicated that cells of c5 and c9 developed towards two directions: one was developed as cells of c2 and c8 and another was developed as those of c1 c6 c7 and c10 ( fig 5e supplementary data s20 and s21 ).; notably c2/c8 and c1/c6/c7/c10 cells are on two different branches developed from the mother cells ( supplementary data s21 ) suggesting that cells in the c1/c6/c7/c10 branch are important for garlic bolting.; this proposal is supported by two bolting-related genes asa2g00291 1 ( fig 3c and d ) and asa7g00828 1 ( supplementary data s5 ) that displayed more abundant transcripts in cells on the c1/c6/c7/c10 branch than on the other branch c2/c8 ( fig 5g ).; expression of asa3g03399 1 can be induced by exposure to a cold environment but after ~6 days of low-temperature exposure its expression level begins to steadily decrease ( supplementary data s22 ).; overexpression of asa3g03399 1 altered flowering time in transgenic arabidopsis plants unexposed to low temperatures ( supplementary data s23 ).; moreover the early flowering phenotype of asa3g03399 1- overexpressed arabidopsis was found to be independent of photoperiod conditions ( supplementary data s23 ).; to identify genes associated with flower development in garlic we compared the expression profiles of flowers at three different developmental stages (early middle and late) from the fertile accession f87 (transcriptome data reported by shemesh-mayer et al [ ]) and identified 2531 and 2066 genes with expression changes from the early stage to the middle stage of flower growth and from the middle to late stage of flower differentiation respectively ( supplementary data s24 ; supplementary data tables s12 and s13 ) indicating that these genes are potentially involved in flower development.; we found that 134 123 and 70 flower genesis-related genes underwent distinct selection in cg1 cg2 and g4 respectively including 18 genes with significant selective signals in two of the garlic groups ( supplementary data s25 ).; notably of these degs related to flower development many are homologous to known cell wall biosynthesis genes and have undergone distinct selection during garlic evolution history including irx12 -like asa2g01537 1 (cg1) and irx9 -like asa6g03949 1 (cg2; fig 6b and c supplementary data s26 ).; in addition 21 garlic nac genes displayed expression differences between different stages of flower development ( supplementary data s27 ) and five of these encoded orthologs of the arabidopsis cell wall formation nac proteins ( fig 6d ) with distinct selection signatures in cg1 ( asa1g04233 1 asa1g04234 1 and asa5g00103 1 ) cg2 ( asa8g04229 1 ) and g4 ( asa5g02353 1 ) ( supplementary data s26 ).; notably these three genes underwent distinct selection in cg1 or cg2 ( fig 6f ; supplementary data s9 )."

"Conflict of interests The authors declare no competing interests."

"This research was supported by grants from the National Natural Science Foundation of China (31872946, 32172566 to H.W., 32372689 to T.L.), the Scientific Research Foundation of Yangzhou University (5018/137012867 to T.L.), the Shandong Provincial Key Research and Development Program (2023CXPT045 to T.L.), and the China Agriculture Research System of MOF and MARA (CARS-24-01 to H.W.)."