Feb 2017

Mapping of quantitative trait loci in pearl millet (Pennisetum glaucum (L.) R. Br.) and relating to the water stress environmentsAparna Kakkera1, Rekha Baddam1, Jana Kholova1, Vincent Vadez1*

1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India

About ICRISAT: www.icrisat.orgICRISAT’s scientific information: http://EXPLOREit.icrisat.org

Table 1. Details of the experiments conducted at Patancheru under well-water and severe water stress conditions

Year TreatmentRainfall (mm)

Stage of crop

during rain Irrigation interval

Total irrigation

(mm)Yield (gm-2)

Mean flowering

time (DAE)

Harvest time (DAE)

2013 Well-water

7 days 420 328 38 77

Mild stress

60 49 DAE 15 days (from 15 DAS)

180 217 37 76

Severe stress

Weekly irrigation till flowering and later

on no irrigation

220 256 38 74

2014 Well-water

7 days 290 300 37 78

13 25 DAE

Mild stress

42 65 DAE 15 days (from 20 DAS)

210 258 36 72

43 75 DAE

Severe stress

Weekly irrigation till flowering and later

on no irrigation

175 168 38 70

Introduction• One well-watered and three different water stress patterns were designed based on the

mean seasonal rain fall variations (460, 305, and 139 mm in 1988) observed during cropping season, in dry environments of Rajasthan, to identify the genomic regions associated with the traits related to stover and grain yield under these varied water stress patterns.

Objectives• To identify the traits that impart yield advantage under different water stress treatments and

QTLs associated with these traits.• To interpret the functional relations of the QTL interactions affecting grain yield under

various water stress treatments.

Figure 1: Traits associated with LG 2

Figure 2: Principal component analysis (PCA) projections on axes 1 and 2 for 113 RILs, estimating the relationship of traits a) account for 64% of total variance under well-water and b) account for 63 % of total variance under severe water stress

Figure 3: QTL interactions from GMM analysis under a) well-water b) mild water stress and c) severe water stress

Figure 4: Traits associated with LG 4 (Fig 4a) and LG 6 (Fig 4b)

PgPb89840.0PgPb1059413.8PgPb860729.8PgPb908145.5PgPb1143363.9PgPb968165.5PgPb9143100.8PgPb11732113.3PgPb10852132.1PgPb9167142.0PgPb10902155.6Xctm03167.7PgPb7431178.4PgPb12731188.5PgPb7979191.8Xpsmp2237193.1PgPb8512196.3PgPb10563198.8PgPb11193200.7PgPb6613 PgPb6558201.2PgPb6013204.5PgPb8369205.8PgPb8177206.6PgPb6628 PgPb7120207.0PgPb7413211.7Xipes0007218.4PgPb6184219.5PgPb11036221.1PgPb10525222.1PgPb6471222.6Xicmp3056223.1PgPb10361224.5Xipes0117225.0PgPb8259226.0PgPb8902231.8PgPb12641240.3PgPb6880242.2PgPb8268248.8PgPb9046255.2PgPb9970256.1PgPb8464 PgPb10086258.7PgPb8139260.7PgPb11702263.8PgPb8214266.5PgPb8035271.1PgPb9474274.9PgPb13146277.9PgPb8457287.0PgPb8244295.6PgPb9338299.1Xipes0003303.5PgPb11641304.9PgPb6117305.4PgPb9306307.5PgPb7336309.6PgPb11469315.3Xctm21318.7PgPb10526320.5PgPb8443322.3PgPb6665322.7PgPb13198324.4PgPb11611327.1Xpsmp2059327.5PgPb12897328.5PgPb8694331.9PgPb7330335.9Xipes0210 Xipes0218341.5PgPb6669344.6PgPb8856349.3PgPb12598351.6PgPb7028355.3PgPb7861355.7PgPb7019 PgPb13134363.1PgPb10206365.4Xipes0118370.3

Locus introgressed to NILsHash et al. 1999

Grain mass_WW

Grain mass_MS

Grain number_WW

Grain number_WW

Grain number_MS

Grain mass_MS

PHI_SS

Tiller number_MS

Tiller number_WW

LG 2

Figure 1: Traits associated with LG 2

Allele from H 77/833–2 parent_unadapted to terminal water stress

Allele from PRLT 2/89–33 parent_adapted to terminal water stress

PgPb89840.0PgPb1059413.8PgPb860729.8PgPb908145.5PgPb1143363.9PgPb968165.5PgPb9143100.8PgPb11732113.3PgPb10852132.1PgPb9167142.0PgPb10902155.6Xctm03167.7PgPb7431178.4PgPb12731188.5PgPb7979191.8Xpsmp2237193.1PgPb8512196.3PgPb10563198.8PgPb11193200.7PgPb6613 PgPb6558201.2PgPb6013204.5PgPb8369205.8PgPb8177206.6PgPb6628 PgPb7120207.0PgPb7413211.7Xipes0007218.4PgPb6184219.5PgPb11036221.1PgPb10525222.1PgPb6471222.6Xicmp3056223.1PgPb10361224.5Xipes0117225.0PgPb8259226.0PgPb8902231.8PgPb12641240.3PgPb6880242.2PgPb8268248.8PgPb9046255.2PgPb9970256.1PgPb8464 PgPb10086258.7PgPb8139260.7PgPb11702263.8PgPb8214266.5PgPb8035271.1PgPb9474274.9PgPb13146277.9PgPb8457287.0PgPb8244295.6PgPb9338299.1Xipes0003303.5PgPb11641304.9PgPb6117305.4PgPb9306307.5PgPb7336309.6PgPb11469315.3Xctm21318.7PgPb10526320.5PgPb8443322.3PgPb6665322.7PgPb13198324.4PgPb11611327.1Xpsmp2059327.5PgPb12897328.5PgPb8694331.9PgPb7330335.9Xipes0210 Xipes0218341.5PgPb6669344.6PgPb8856349.3PgPb12598351.6PgPb7028355.3PgPb7861355.7PgPb7019 PgPb13134363.1PgPb10206365.4Xipes0118370.3

Locus introgressed to NILsHash et al. 1999

Grain mass_WW

Grain mass_MS

Grain number_WW

Grain number_WW

Grain number_MS

Grain mass_MS

PHI_SS

Tiller number_MS

Tiller number_WW

LG 2

Figure 1: Traits associated with LG 2

Allele from H 77/833–2 parent_unadapted to terminal water stress

Allele from PRLT 2/89–33 parent_adapted to terminal water stress

b)

Fig 4aPgPb101840.0PgPb113257.5PgPb1171118.1PgPb1316123.8PgPb1029233.9PgPb990341.0PgPb663741.9PgPb989450.2PgPb978852.1PgPb1000552.5PgPb1103155.2PgPb993359.8PgPb1094663.6PgPb623066.2PgPb1074671.2PgPb710172.1PgPb791073.8PgPb771179.9PgPb1136790.9PgPb1011094.8PgPb795895.8PgPb1260897.5PgPb647898.1PgPb13415100.1Xipes0186101.5PgPb6893102.4PgPb9293103.8Xicmp3029105.4PgPb10768106.4PgPb13178107.4Xipes0066 PgPb7832

PgPb13377108.3

PgPb7642109.1Xpsmp2084109.9PgPb10141111.2PgPb10598112.0PgPb7545112.9Xipes0076113.8PgPb12205114.7PgPb10552118.3PgPb9450123.0PgPb8656127.1PgPb7528134.4PgPb8208143.1PgPb7311155.2PgPb6639156.1

FT, SV_ WW, MS

HI_ WW, MS, SS

LG 4 Fig 4b LG 6PgPb130620.0

Xicmp30024.7

PgPb69476.2

PgPb708212.3

PgPb801813.7

PgPb5969 PgPb8664

PgPb1071514.2

PgPb8306 PgPb913919.7

Xipes017620.2

PgPb1026421.1

PgPb1194721.6

PgPb1232222.5

PgPb9775 PgPb1076723.4

PgPb836826.5

PgPb1047030.4

PgPb10723 PgPb10580

Xipes007131.5

PgPb1311332.0

PgPb693137.0

PgPb891942.2

PgPb751644.0

PgPb923544.9

PgPb12466 Xicmp305046.9

Xipes008747.5

PgPb860148.0

PgPb893550.8

PgPb1316451.2

Xpsmp227054.1

PgPb1060364.0

PgPb11645 PgPb1156366.8

PgPb641669.4

PgPb989877.1

PgPb1139781.7

FT

Grain yield_SS

PHI_MS, SS

Grain yield_WW, MS

Grain no_MS

a) b)

Results• Grain mass, grain number and tiller

number were linked to terminal drought tolerant region of LG 2 under all the moisture treatments (Fig 1).

• Grain number showed very close relationship with grain yield under well-water conditions (Fig 2a)

• Tiller number comapped with grain number and also showed a close relationship with grain yield under well-water conditions.

• Grain mass has its importance as the water stress becomes severe (Fig 2b)

• Under severe water stress, grain mass, grain number and PHI showed a close relationship with grain yield

Epistatic interactions for grain yield:• A combination of tiller number,

PHI and SY alleles showed 17-21% increase in grain yield under well-water conditions (Fig 3a)

• Under mild water stress conditions also a combination of tiller number, HI and SY alleles showed 29% increase in grain yield (Fig 3b)

• Under severe stress a combination of grain mass, HI and PHI alleles showed 8% increase in grain yield (Fig 3c)

a)

For more details contact v.vadez@cgiar.org

b)a)

17%

Well-water

(19.7 cM, p_8306) FT, PHI Tillers21%

a)

Mild water stress

29%

(76.78 cM, p_12113)

(286.98 cM, p_8457)

(51.48 cM, p_13164)

b)

Severe water stress

8%

(101.97 cM, p_9343)

(31.46 cM, p_10723)

(24.39 cM, p_8170)

c)

c)

Materials and Methods• Phenotypic

evaluation was carried out on 113 F7 progenies of RIL cross H 77/833-2 X PRLT 2/89-33. Test cross hybrids of this cross were grown under well-water (WW), mild stress (MS) and severe water stress (SS) environments in the fields of ICRISAT-Patancheru during 2013 and 2014 (Table 1).

• The genotyping of F6 plants of the RIL cross H 77/833–2 x PRLT 2/89–33 was used for construction of linkage map. The linkage map consists of 321 markers distributed across seven linkage groups (LG), with an average marker interval length 3.7cM. Phenotyping and genotyping data was subjected to QTL mapping through composite interval mapping approach of PLABQTL.

Conclusions• Terminal drought tolerant region identified on LG 2 was associated with grain yield components

i.e. grain mass, grain number of all the moisture treatments, tiller number (mild water stress) and PHI (severe water stress).

• Stover yield (SY) and flowering time (FT) were majorly associated with LG 4 and LG 6 (mild water stress).

• Under well-water and mild water stress, grain number and tiller number were favourable for retaining grain yield.

• Grain mass is more favourable for retaining grain yield under severe water stress, i.e. alleles favouring the ability of filling grains would be the choice of selection under severe water stress environments.