Rice Science ›› 2017, Vol. 24 ›› Issue (4): 198-206.DOI: 10.1016/j.rsci.2017.01.002
• Orginal Article • Previous Articles Next Articles
S. M. Masuduzzaman A.1, Maksudul Haque Md.2(), K. M. Shamsuddin A.3, A. Salam M.1, Ansar Ali Md.4
Received:
2016-10-06
Accepted:
2017-01-13
Online:
2017-07-10
Published:
2017-04-28
S. M. Masuduzzaman A., Maksudul Haque Md., K. M. Shamsuddin A., A. Salam M., Ansar Ali Md.. Haplotype Diversity at Sub1 Locus and Allelic Distribution Among Rice Varieties of Tide and Flood Prone Areas of South-East Asia[J]. Rice Science, 2017, 24(4): 198-206.
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Sub1A locus | Sub1C locus | |||||||
---|---|---|---|---|---|---|---|---|
Sub1A0 | Sub1A1 | Sub1A2 | Sub1C1 | Sub1C2 | Sub1C3 | Sub1C4 | ||
Allele size before digestion (bp) | - | 241 | 241 | 175 | 165 | 170 | 175 | |
Allele size after digestion (bp) | - | 241 | 134, 107 | 130, 45 | 110, 55 | 110, 60 | 110, 65 | |
Account | 89 | 16 | 55 | 12 | 83 | 6 | 59 | |
Frequency (%) | 55.6 | 10 | 34.4 | 7.5 | 51.9 | 3.7 | 36.9 |
Table 1 Size and frequency of different variants of Sub1A and Sub1C alleles, before and after digestion with respective enzymes.
Sub1A locus | Sub1C locus | |||||||
---|---|---|---|---|---|---|---|---|
Sub1A0 | Sub1A1 | Sub1A2 | Sub1C1 | Sub1C2 | Sub1C3 | Sub1C4 | ||
Allele size before digestion (bp) | - | 241 | 241 | 175 | 165 | 170 | 175 | |
Allele size after digestion (bp) | - | 241 | 134, 107 | 130, 45 | 110, 55 | 110, 60 | 110, 65 | |
Account | 89 | 16 | 55 | 12 | 83 | 6 | 59 | |
Frequency (%) | 55.6 | 10 | 34.4 | 7.5 | 51.9 | 3.7 | 36.9 |
Fig. 1. Sub1A0, Sub1A1 and Sub1A2 alleles among varieties. A, Single allele before digestion with Alu I; B, Two allelic variants after digestion with Alu I.IR40931 and IR42 have tolerant and intolerant allele, respectively.
Fig. 2. Allelic patterns generated at Sub1A.Sub1A1, Fragment without restriction site; Sub1A2, Red mark indicates a single nucleotide polymorphism at a specific site in the DNA sequence; Sub1A0, A null allele that completely lacks the gene’s normal function.
Fig. 3. Sub1C alleles among varieties. A, Three allelic variants before digestion with Cac8 I; B, Four allelic variants after digestion with Cac8 I. IR40931, IR42, Lemo, Matichak have Sub1C1, Sub1C2, Sub1C3, and Sub1C4 alleles, respectively. Sub1C1, 175 bp is cut into 130 and 45 bp (tolerant specific); Sub1C4, 175 bp is cut into 110 and 65 bp (intolerant specific); Sub1C3, 170 bp is cut into 110 and 60 bp (intolerant specific); Sub1C2, 165 bp is cut into 110 and 55 bp (intolerant specific).
Country/Institute | A1C1 | A1C2 | A1C4 | A2C2 | A2C4 | A0C2 | A0C3 | A0C4 | Total |
---|---|---|---|---|---|---|---|---|---|
Bangladesh | 2 | 2 | 1 | 22 | 0 | 15 | 1 | 7 | 50 |
India | 2 | 1 | 0 | 4 | 1 | 2 | 0 | 4 | 14 |
Sri Lanka | 7 | 0 | 0 | 6 | 0 | 0 | 1 | 2 | 16 |
Indonesia | 0 | 0 | 0 | 19 | 1 | 9 | 3 | 37 | 69 |
Vietnam | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 5 | 7 |
IRRI | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 4 |
Total | 12 | 3 | 1 | 53 | 2 | 27 | 6 | 56 | 160 |
Frequency (%) | 7.5 | 1.9 | 0.6 | 33.1 | 1.3 | 16.9 | 3.7 | 35 | 100 |
Table 2 Pattern of haplotype frequencies and their distributions.
Country/Institute | A1C1 | A1C2 | A1C4 | A2C2 | A2C4 | A0C2 | A0C3 | A0C4 | Total |
---|---|---|---|---|---|---|---|---|---|
Bangladesh | 2 | 2 | 1 | 22 | 0 | 15 | 1 | 7 | 50 |
India | 2 | 1 | 0 | 4 | 1 | 2 | 0 | 4 | 14 |
Sri Lanka | 7 | 0 | 0 | 6 | 0 | 0 | 1 | 2 | 16 |
Indonesia | 0 | 0 | 0 | 19 | 1 | 9 | 3 | 37 | 69 |
Vietnam | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 5 | 7 |
IRRI | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 4 |
Total | 12 | 3 | 1 | 53 | 2 | 27 | 6 | 56 | 160 |
Frequency (%) | 7.5 | 1.9 | 0.6 | 33.1 | 1.3 | 16.9 | 3.7 | 35 | 100 |
Fig. 4. Allelic patterns generated at Sub1C after digestion with Cac8 I.Restriction region is red at different positions. After digestion with Cac8 I, four allelic variants were found.
Haplotype | Representative variety | Phenotype | Average of elongation score | Average survival rate (%) | Elongation rate (%) |
---|---|---|---|---|---|
A1C1 | FR13A | SE/T | 2.3 | 94 | 37 |
Motorsail | ME/MT | 5.1 | 59 | 78 | |
Gopalbhag | HE/MS | 7.3 | 36 | 93 | |
A2C2 | Madabaru Kottamali | ME/MT | 3 | 74 | 56 |
Habiganj Aman 7 | HE/S | 7.7 | 18 | 212 | |
A0C2 | Badal | ME/MT | 4.3 | 52 | 64 |
Fulkari | HE/S | 7.3 | 0 | 167 | |
A0C4 | Kannimurunga | ME/MT | 5.3 | 63 | 72 |
Kumragoir | HE/S | 9 | 17 | 123 | |
A1C2 | Lalchikon | SE/MT | 4.5 | 58 | 47 |
A1C4 | Matichak | ME/MT | 5 | 60 | 80 |
A2C4 | CN540 | HE/S | 9 | 26 | 102 |
A0C3 | Ketumbar | HE/S | 8.7 | 7 | 110 |
Table 3 Association of haplotype patterns with phenotype (elongation and survival).
Haplotype | Representative variety | Phenotype | Average of elongation score | Average survival rate (%) | Elongation rate (%) |
---|---|---|---|---|---|
A1C1 | FR13A | SE/T | 2.3 | 94 | 37 |
Motorsail | ME/MT | 5.1 | 59 | 78 | |
Gopalbhag | HE/MS | 7.3 | 36 | 93 | |
A2C2 | Madabaru Kottamali | ME/MT | 3 | 74 | 56 |
Habiganj Aman 7 | HE/S | 7.7 | 18 | 212 | |
A0C2 | Badal | ME/MT | 4.3 | 52 | 64 |
Fulkari | HE/S | 7.3 | 0 | 167 | |
A0C4 | Kannimurunga | ME/MT | 5.3 | 63 | 72 |
Kumragoir | HE/S | 9 | 17 | 123 | |
A1C2 | Lalchikon | SE/MT | 4.5 | 58 | 47 |
A1C4 | Matichak | ME/MT | 5 | 60 | 80 |
A2C4 | CN540 | HE/S | 9 | 26 | 102 |
A0C3 | Ketumbar | HE/S | 8.7 | 7 | 110 |
Fig. 5. Recovery of varieties after submergence.IR40931 is as the tolerant check (A1C1), Madabaru is as the moderately tolerant check (A2C2) and IR42 is as the intolerant check (A2C2). A, 7 d after de-submergence; B, 14 d after de-submergence; C, 40 d after de-submergence.
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