Figures (5)  Tables (6)

    • Figure 1. 

      The distribution and quantity information of different repeat types of SSRs in the reference genome of seashore paspalum.

    • Figure 2. 

      The most abundant motif categories in the reference genome of seashore paspalum.

    • Figure 3. 

      Distribution of perfect SSRs in different region of seashore paspalum reference genome.

    • Figure 4. 

      Amplification of 33 collections of seashore paspalum with the SSR primers SPR75. M: 500-bp DNA marker; 1−33: SP001−SP110.

    • Figure 5. 

      UMPGA genetic clustering of 33 collections of seashore paspalum based on SSR molecular markers.

    • No. Germplasm ID Type or cultivar Source
      1 SP001 Seaspray Hainan, China
      2 SP002 Salam Hainan, China
      3 SP004 SeaIsle 2000 Zhejiang, China
      4 SP005 Breeding material Radiation mutagenesis
      5 SP006 Adalayd-2 Guangdong, China
      6 SP019 Mauna key USA
      7 SP022 HI 26 USA
      8 SP035 AM3554 USA
      9 SP036 Temple 1 USA
      10 SP041 Grif 15191 Brazil
      11 SP107 Breeding material USA
      12 SP052 Breeding material Radiation mutagenesis
      13 SP053 Breeding material Radiation mutagenesis
      14 SP061 Breeding material Anhui, China
      15 SP083 Breeding material Hainan, China
      16 SP084 Breeding material Hainan, China
      17 SP089 Breeding material Hainan, China
      18 SP090 Breeding material Hainan, China
      19 SP091 Breeding material Guangxi, China
      20 SP092 Breeding material Guangxi, China
      21 SP093 Breeding material Hainan, China
      22 SP094 Breeding material Guangxi, China
      23 SP095 Breeding material Fujian, China
      24 SP096 Breeding material Anhui, China
      25 SP097 Breeding material Zhejiang, China
      26 SP098 Breeding material Shanghai, China
      27 SP099 Breeding material Fujian, China
      28 SP100 Breeding material Hainan, China
      29 SP102 Breeding material USA
      30 SP103 Breeding material Hainan, China
      31 SP106 Breeding material Jiangsu, China
      32 SP108 Breeding material Hainan, China
      33 SP110 Breeding material Jiangsu, China

      Table 1. 

      Information of 33 germplasm sources of seashore paspalum.

    • Item Description Number
      Total number of sequences Counts 1,902
      Total length of sequences A + T + C + G + N (bp) 646,899,508
      Total valid length of sequences A + T + C + G (bp) 643,809,508
      Unkown bases (Ns) in sequences Bp 3,090,000
      Percentage of unkown bases Percentage (%) 0.48
      GC content Not include Ns (%) 45.9

      Table 2. 

      Summary of the genomic information of seashore paspalum.

    • Item Description Number
      Total number of perfect SSRs Counts 94,748
      Total length of perfect SSRs Bp 1,400,913
      The average length of SSRs Total SSR length/total SSR counts (bp) 14.79
      SSRs per sequence Total SSR counts/sequence counts 50
      The percentage of sequence covered by SSRs Total SSR length/total sequence length (%) 0.22
      Relative abundance Total SSRs/total valid length (loci/Mb) 147.17
      Relative density Total SSR length/total valid length (bp/Mb) 2,175.97

      Table 3. 

      Frequency information of SSRs in the reference genome of seashore paspalum.

    • Type Counts Length (bp) Percent (%) Average length (bp) Relative dbundance (loci/Mb) Relative density (bp/Mb)
      Mono 53,595 621,084 56.57 11.59 83.25 964.7
      Di 22,044 409,090 23.27 18.56 34.24 635.42
      Tri 16,047 282,576 16.94 17.61 24.93 438.91
      Tetra 2,086 55,620 2.2 26.66 3.24 86.39
      Penta 579 16,835 0.61 29.08 0.9 26.15
      Hexa 397 15,708 0.42 39.57 0.62 24.4
      Mono, Di, Tri, Tetra, Penta, and Hexa refer to the types of simple sequence repeats (SSRs) with one, two, three, four, five, and six nucleotide repeats, respectively. The same abbreviations will be used throughout.

      Table 4. 

      Description of different types of SSRs in the reference genome of seashore paspalum.

    • Chromosome Maker mapped Chromosome Maker mapped
      CM.08 10,591 CM.14 5,991
      CM.09 8,841 CM.15 4,498
      CM.10 8,849 CM.16 6,282
      CM.11 7,670 CM.17 6,635
      CM.12 7,676 All 85,955
      CM.13 6,399

      Table 5. 

      Distribution of SSR primers in the chromosomes of the seashore paspalum reference genome.

    • Marker Repeat motif Forward primer Reverse primer Tm (°C) Product size (bp) Na Ne I Nei's
      SPR5 (GGA) 8 GAGAAGGTGACGAGGAGGC TTCAAAAGTTTGCGGACCGG 59 219 2.00 1.98 0.69 0.50
      SPR6 (CT) 9 CGATCGCTTCATGGGAGTGG GCCTAGCTAGCTCTGCATCC 60 188 2.00 1.98 0.69 0.50
      SPR10 (GA) 10 CCTTCGTTCAGTTCAGCTGC GACCAAATTCAAGGCCCACC 59 144 2.00 1.98 0.69 0.50
      SPR11 (TG) 11 TGGGCTAAGCAAGGATGAGG AGTGATGTACAGCTGCTGCC 59 136 2.00 1.50 0.52 0.33
      SPR15 (ATCT) 20 ACCAGAAACTAGCGAGGTAGC AAGATGATCAGCAGTGCCCC 59 187 2.00 1.84 0.65 0.46
      SPR16 (GAG) 11 ACTACACTAATCGGCGGTCG TGGACTTTGGACGTCGTTCC 59 171 2.00 1.50 0.52 0.33
      SPR18 (AT) 26 TCTGTAGTGGTATGCGCACG CACTTTTACAGTTGCGGGGC 60 172 4.00 2.34 1.03 0.57
      SPR26 (AT) 25 GGAGGCACTGTCTAGTATGTGG GCGACTGAATGTTCTGGACC 59 188 2.00 2.00 0.69 0.50
      SPR27 (AT) 28 GGACTGCAGGAACTTTTGAGC CGATCCACTCTCTTTTCTTTCTCC 59 197 3.00 2.06 0.76 0.51
      SPR28 (AGC) 7 GAATGGCGCTTGAGTTGAGC CAGGATCCCCAAGGTGAGC 60 144 2.00 1.35 0.43 0.26
      SPR31 (AAG) 20 ATGCCCGTACTTAGGAAGGC TTAATCCACGGTAGGGGTGC 59 235 2.00 1.46 0.50 0.32
      SPR57 (CGGC) 7 TAACTCGTCGTCGTCTCACG ACTGACGAAGGATGGATGCG 59 135 2.00 1.10 0.18 0.09
      SPR63 (TTAGA) 7 CGTGCTACATGTCCGTGGG TTGCGCTTAATGATGGCTCC 60 135 2.00 1.08 0.17 0.08
      SPR75 (GGAT) 5 CCCATGCGTGCTCAATAACG ACATACACCACACCGTACCG 59 167 2.00 1.13 0.23 0.11
      Average 2.21 1.66 0.55 0.36

      Table 6. 

      Information of marker and genetic diversity.