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Table 2 Features of genes involved in seed coat permeability selected for further analysis (Chr. No. - Chromosome Number; bp – base pairs)

From: Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

Gene (Glyma Ids)

Gene length (bp)

Variation position (Chr No.: start position coordinates)

Variation identified (G.max / G.soja)

Variation effect (G. max/G. soja amino acid change) on protein

Impact of variability

Anthranilate n-hydroxy cinnamoyl/benzoyl transferase (Glyma17g16330)

4249

17:12977991

−−−/AAA

(−/K)

Moderate

Chalcone flavone isomerase (Glyma03g31100)

6050

3:38990976

−−−−−−−−−/ACGGCCACG

(−/VAV)

Moderate

Abscisic Acid Insensitive 5 (Glyma19g37910)

5266

19:45001036

−−−/GGT

(−/G)

Moderate

PhospholipaseD (Glyma20g38200)

10,132

20:45855223

−−−/TTG

(−/L)

Moderate

TypeI- Inositol polyphasphate 5 phosphotase1 (Glyma02g08620)

7867

2:6711434

−−−−−−−−−−−−/GGACAACAGGCA

(−/DNRC)

Moderate

E3 ubiquitin ligase (Glyma10g43120)

4938

10:49932855

−−−−−−−−−−/TATAGATATA

Stop codon gain, Protein truncation (P/L*IYX)

High

Glycosyl transferase (Glyma13g05441)

5969

13:5763533

−−/TA (Insertion is present upstream to gene)

–

Moderate