*morphological identification. NP = not provided, MAP = months after planting.*

#### **Table 1.**

**9**

*Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer's Fields: An Update…*

polymorphisms, independent of the physiological status of the plant or the environ-

Since the mid 80's, molecular markers have been used in cassava for a large number of genetic diversity and variety identification studies (**Table 2**). The scientific community working on cassava is therefore well acquainted with the development and use of these markers [64, 71–74, 78, 81, 126, 127, 131, 135–140]. The first

attempt to use molecular markers for variety identification in crops was undertaken at CIAT by Hussain et al. [131], Ramirez et al. [139], and Ocampo et al. [122], using isozymes. In 1992, Ocampo et al. [122], using αβ-esterase isozymes, analyzed 86% of the global cassava collection of 4,034 *M. esculenta* accessions maintained at CIAT, and found 2,158 accessions (50%) with 2 to 39 clones sharing the same banding pattern. These results highlight the need to analyze morphological and molecular data

In 1995, Ocampo et al. [121] implemented a DNA fingerprinting method for genetic analysis called restriction fragment length polymorphisms (RFLPs). RFLPs allowed Ocampo et al. [121] to estimate the number of duplicates in the CIAT collection; of the 5500 genotype approximately 1,000 could be duplicates indicating an approximate 18% redundancy in the global germplasm collection (**Table 2**). Therefore, the RFLP marker system is an attractive approach because they are inherited in a co-dominant mode, allowing homozygotes to be distinguished from heterozygotes, and are locus-specific and highly informative, targeting specific sites on the genome, due to restriction-site specificity [123]. However, the use of RFLPs can be challenging, as their use is laborious, costly, and can only resolve mutations at the enzyme cut site, limiting their use in phylogenetic reconstruction [123]. Nevertheless, these efforts demonstrate that the identification of genetic variety can be achieved using molecular genetic tools, and used for germplasm management,

together, to gradually eliminate duplicates from the germplasm collection.

including quality control of experimental lines across breeding programs.

reported by Ocampo and co-workers [121].

[141], allowed cassava scientists at CIAT to investigate genetic differences using minute amounts of DNA, coupled with random primer amplification to produce random amplified polymorphic DNA (RAPD) [70, 83, 86, 126, 142, 143]. RFLPs were therefore superseded by PCR-based markers [127]. Since then, other PCRbased molecular markers tools have been adapted and deployed, such as amplified fragment length polymorphisms (AFLPs) [72, 73], inter-simple sequence repeats (ISSRs) [56, 115, 117], single sequences repeats (SSRs) [71, 73, 74, 78], sequencerelated amplified polymorphisms (SRAPs) [94], inter-sequence tagged repeats (ISTRs) [86], and diversity arrays technology (DArT) [67]. Over the past 30 years, SSRs have been the molecular marker approach most widely used in cassava, both for variety identification and to estimate the genetic diversity of the crop (**Table 2**). Chavarriaga-Aguirre et al. [73], used this approach to search for duplicates in the CIAT's core collection, but reported a lower frequency of duplicates than was

The release of the cassava reference genome by Prochnik et al. [144] allowed cassava geneticists in Africa and LAC to identify tens of thousands genome-wide sequence variations across multiple landraces and improved cultigens [2, 145, 146]. These genomic variations were unraveled by re-sequencing using restriction-site associated DNA-sequencing (RAD-seq) [145] or genotyping by sequencing (GBS) [147]. These two methods can detect small genetic differences between individuals, and therefore may be useful for studying organisms with reduced genetic

The polymerase chain reaction (PCR) technique, published in 1986 by Mullis et al.

*DOI: http://dx.doi.org/10.5772/intechopen.99110*

**3. Molecular markers deployed in cassava**

mental conditions in which it grows.

*The literature pertaining to cassava (rev. ref.) on agro-morphological characterization reviewed in this paper.* polymorphisms, independent of the physiological status of the plant or the environmental conditions in which it grows.

#### **3. Molecular markers deployed in cassava**

*Cassava - Biology, Production, and Use*

**Morphological Descriptors**

**Scoring** 

**No. of variables**

**No. of** 

**Dupl.**

**Schedule**

**QLT**

**QNT**

**No.**

56

NP

6

2

0

[34]

**Rev. Ref.**

**8**

**Region**

Asia SEA

Indonesia

Vietnam

Pacific

Vanuatu

Islands

(Oceania)

*morphological identification. NP = not provided, MAP = months after planting.*

*The literature pertaining to cassava (rev. ref.) on agro-morphological characterization reviewed in this paper.*

**Table 1.**

India

**Location**

**Cassava** *(M. esculenta)*

**Source** Western Ghats region of Tamil Nadu, covering 32 villages in the southern

region of Western Ghats with altitude ranging from 250 to 2552 feet above

MSL

Field collected in Java, Sumatera, Kalimantan, Sulawesi, Maluku, Nusa

181

7 145

12MAP

12

0

4

[36]

4–8 MAP

20

0

0

[20]

12 MAP

10

0

0

[33]

Tenggara Timur and Papua Islands

Collection maintained at the Root Crop Research and Development Center

(RCRDC), and Field Crops Research Institute, located in Chuong My, Hanoi

Collection maintained at Vanuatu Agricultural Research and Training Centre

(VARTC)

*The number of cassava (M. esculenta) varieties identified in Africa, LAC, Asia, SEA, and Oceania, as well as the number of qualitative (QLT) and quantitative (QNT) descriptors used for the* 

Since the mid 80's, molecular markers have been used in cassava for a large number of genetic diversity and variety identification studies (**Table 2**). The scientific community working on cassava is therefore well acquainted with the development and use of these markers [64, 71–74, 78, 81, 126, 127, 131, 135–140]. The first attempt to use molecular markers for variety identification in crops was undertaken at CIAT by Hussain et al. [131], Ramirez et al. [139], and Ocampo et al. [122], using isozymes. In 1992, Ocampo et al. [122], using αβ-esterase isozymes, analyzed 86% of the global cassava collection of 4,034 *M. esculenta* accessions maintained at CIAT, and found 2,158 accessions (50%) with 2 to 39 clones sharing the same banding pattern. These results highlight the need to analyze morphological and molecular data together, to gradually eliminate duplicates from the germplasm collection.

In 1995, Ocampo et al. [121] implemented a DNA fingerprinting method for genetic analysis called restriction fragment length polymorphisms (RFLPs). RFLPs allowed Ocampo et al. [121] to estimate the number of duplicates in the CIAT collection; of the 5500 genotype approximately 1,000 could be duplicates indicating an approximate 18% redundancy in the global germplasm collection (**Table 2**). Therefore, the RFLP marker system is an attractive approach because they are inherited in a co-dominant mode, allowing homozygotes to be distinguished from heterozygotes, and are locus-specific and highly informative, targeting specific sites on the genome, due to restriction-site specificity [123]. However, the use of RFLPs can be challenging, as their use is laborious, costly, and can only resolve mutations at the enzyme cut site, limiting their use in phylogenetic reconstruction [123]. Nevertheless, these efforts demonstrate that the identification of genetic variety can be achieved using molecular genetic tools, and used for germplasm management, including quality control of experimental lines across breeding programs.

The polymerase chain reaction (PCR) technique, published in 1986 by Mullis et al. [141], allowed cassava scientists at CIAT to investigate genetic differences using minute amounts of DNA, coupled with random primer amplification to produce random amplified polymorphic DNA (RAPD) [70, 83, 86, 126, 142, 143]. RFLPs were therefore superseded by PCR-based markers [127]. Since then, other PCRbased molecular markers tools have been adapted and deployed, such as amplified fragment length polymorphisms (AFLPs) [72, 73], inter-simple sequence repeats (ISSRs) [56, 115, 117], single sequences repeats (SSRs) [71, 73, 74, 78], sequencerelated amplified polymorphisms (SRAPs) [94], inter-sequence tagged repeats (ISTRs) [86], and diversity arrays technology (DArT) [67]. Over the past 30 years, SSRs have been the molecular marker approach most widely used in cassava, both for variety identification and to estimate the genetic diversity of the crop (**Table 2**). Chavarriaga-Aguirre et al. [73], used this approach to search for duplicates in the CIAT's core collection, but reported a lower frequency of duplicates than was reported by Ocampo and co-workers [121].

The release of the cassava reference genome by Prochnik et al. [144] allowed cassava geneticists in Africa and LAC to identify tens of thousands genome-wide sequence variations across multiple landraces and improved cultigens [2, 145, 146]. These genomic variations were unraveled by re-sequencing using restriction-site associated DNA-sequencing (RAD-seq) [145] or genotyping by sequencing (GBS) [147]. These two methods can detect small genetic differences between individuals, and therefore may be useful for studying organisms with reduced genetic


**11**

**Region** Africa

C D D&E

E F G D H B D I E I B J C I D K I I G L

19

102

**X**

18

547

2&11

87

**X**

1, 2&11

89

17

96

**X**

**X** **X**

16

7376

15

981

2&14

327

**X**

13

12

**X**

12

10

11

320

10

21

9

43

**X**

2

24

**X** **X** **X** **X** **X** **X**

1&2

53

8

93

**X**

2

63

7

288

**X**

6

28

5

24

4

283

2

29

3

365

**X**

**Location**

**Source**

**No. of cassava samples**

**Morphological Descriptors**

**Isozymes**

**RFLPs**

**RAPDs**

**SSRs**

**ISSRs**

**SRAPs**

**ISTR**

**AFLPs**

**DaRTs**

**SNPs**

**No. of Duplicates**

181

10 0 0 1 0 0 5

> **X**

0 10

1 0 1 0 163

> **X**

**X**

2594

22 0

> **X**

**X** **X**

0

[112]

461

[116]

9

[119]

[118]

[16]

[63]

629

[2]

[15]

[56]

[104]

[106]

[58]

[49]

[101]

[50]

[59]

[91]

[53]

[83]

[81]

[66]

**X**

> **X**

> > **X**

**X** **X** **X**

**X** **X**

**X**

[124]

**Rev. Ref.**

*Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer's Fields: An Update…*

*DOI: http://dx.doi.org/10.5772/intechopen.99110*

[86]

#### *Cassava - Biology, Production, and Use*

*Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer's Fields: An Update… DOI: http://dx.doi.org/10.5772/intechopen.99110*


*Cassava - Biology, Production, and Use*

**10**

**Region** Global

A A A A A A A A B

1&2

74

1

38

1

521

**X**

**X**

1

552

1

105

**X**

1

7

1

88

1

4304

1

19

**X** **X** **X** **X**

**X** **X** **X**

**X**

**X**

**Location**

**Source**

**No. of** 

**Morphological** 

**Isozymes**

**RFLPs**

**RAPDs**

**SSRs**

**ISSRs**

**SRAPs**

**ISTR**

**AFLPs**

**DaRTs**

**SNPs**

**No. of** 

**Rev.** 

**Duplicates**

0 2158

51 0 0 0 19 0

> **X**

0

[89]

[71]

[73]

[74]

[72]

**X**

[70]

[121]

[122]

[131]

**Ref.**

**cassava** 

**Descriptors**

**samples**


**13**

**Region**

LAC

P S P P P P P P P A T P P A P P P P P P

25

3354

47

144

46

106

45

303

25

2731

44

51

43

436

42

121

41

60

1&40

163

**X** **X** **X** **X** **X** **X** **X**

39

173

**X**

25

1280

36

16

**X**

38

419

**X**

37

36

36

16

**X**

33&41

20

25

93

35

185

34

14

**X**

**X** **X** **X** **X** **X** **X** **X**

> **X**

**Location**

**Source**

**No. of cassava samples**

**Morphological Descriptors**

**Isozymes**

**RFLPs**

**RAPDs**

**SSRs**

**ISSRs**

**SRAPs**

**ISTR**

**AFLPs**

**DaRTs**

**SNPs**

**No. of Duplicates**

0 2 4 0 0 19 0 0

> **X**

**X**

20

0 1 5

> **X**

316

0

> **X**

614

18 4 0

> **X**

1818

[65]

[114]

[113]

[120]

[134]

[110]

[4]

[109]

[125]

[108]

[105]

0

[103]

[55]

[54]

[61]

[97]

[96]

[95]

[51]

**Rev. Ref.**

*Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer's Fields: An Update…*

*DOI: http://dx.doi.org/10.5772/intechopen.99110*

[99]

#### *Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer's Fields: An Update… DOI: http://dx.doi.org/10.5772/intechopen.99110*


*Cassava - Biology, Production, and Use*

**12**

**Region**

Asia

M M M M N M M

EU

O O

> LAC

P Q

P P Q

P P P R A P R P P

33

83

32

42

30

145

31

137

**X**

**X** **X** **X** **X**

1

33

30

66

29

20

**X** **X**

28

117

27

28

**X** **X**

26

29

**X**

1&25

118

24

54

23

31

22

32

**X**

3

20

3

80

20

14

20

6

21

18

20

45

20

110

**X**

21

58

**X**

**X** **X** **X** **X**

> **X**

> > **X**

**X** **X** **X** **X**

**X**

**X**

**X**

**X**

20

218

**X**

**X**

**Location**

**Source**

**No. of** 

**Morphological** 

**Isozymes**

**RFLPs**

**RAPDs**

**SSRs**

**ISSRs**

**SRAPs**

**ISTR**

**AFLPs**

**DaRTs**

**SNPs**

**No. of** 

**Rev.** 

**Duplicates**

62

2 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0

> **X**

0 42

0 2 1

[98]

[90]

[88]

[69]

[67]

[84]

[85]

[82]

[80]

[68]

[78]

[133]

[76]

**X** **X** **X**

[64]

[126]

[123]

[115]

[117]

[94]

[93]

[132]

[52]

[62]

**Ref.**

**cassava** 

**Descriptors**

**samples**

