Transfer of deeper rooting and phosphorus uptake QTL into the popular rice variety 'maudamani' via marker-assisted backcross breeding

Abstract

Rice suffers from drought stress due to its shallow roots, hindering water uptake from deeper soil layers. Transfer of deeper rooting QTL will modify the root architecture of the plant allowing it to extract moisture from deeper layers of the soil. Furthermore, poor soil conditions, particularly phosphorus deficiency is a common problem in the rainfed rice ecology of India which requires adequate phosphate fertilizer for obtaining higher yield. In this current investigation, two QTL (DRO1 and DRO3) for deeper rooting and one QTL for phosphorus uptake (Pup1) were introgressed into a popular variety, 'Maudamani' through marker-assisted backcross breeding. The target QTL were transferred from a pre-breed genotype, CR3996-19-9-45-1 into the popular variety. Foreground selection was performed using the tightly linked microsatellite markers in the backcross generations progenies to select plants carrying the target QTL. Background selection in each backcross generations was performed using 123 polymorphic SSR markers spread across twelve chromosomes. In each backcross generations, plants carrying all three target QTL and with highest recurrent parent genome recovery percentage was used to backcross with the popular variety, Maudamani. In BC₂F₂ generation, five plants (CR6508-111-101-129, CR6508-111-101-267, CR6508-111-101-413, CR6508-111-101-537 and CR6508-111-101-713) were selected which were homozygous for all three target QTL. The pyramided lines were evaluated for deeper rooting, low phosphorus stress tolerance and various agro-morphologic including quality traits. Progenies of those five pyramided plants showed similarity with the recipient parent for the 14 agro-morphologic and quality traits in their BC₂F₃ and BC₂F₄ generations. The introgressed lines demonstrated significantly improved root traits, including increased number of deeper roots, longer root length and higher shoot and root dry weight, compared to Maudamani under both moisture-deficit and normal conditions. Furthermore, those lines exhibited enhanced phosphorus uptake and grain yield compared to the recipient parent, Maudamani under low phosphorus conditions.

Keywords: DRO1; DRO3; Pup1; Deeper rooting; Marker-assisted breeding; Phosphorus deficiency; Rice.

Fig. 1

PCR amplification of markers RM242 linked to DRO1 and RM5508 linked to DRO3; Pup1-K46, RM28073 and RM28102 linked to low phosphorus tolerance in BC₂F₂ progenies. Molecular weight of markers (50 bp plus Ladder) and lanes of the top of the gel indicate BC₂F₂ progenies.

Fig. 2

(A) Dendrogram showing relatedness among five pyramided lines along with two parents (CR3996-19-9-45-1 and Maudamani) based on agro-morphological and quality traits; (B) Dendrogram showing the genetic relationship between lines based on five microsatellite markers and parents; (C) Percentage contribution of recurrent parent genome in the pyramided lines.

Fig. 3

Graphical genotyping representation of QTL stacking and recipient parent’s genome recovery for the carrier chromosomes associated with deeper rooting and phosphorus uptake QTL in five pyramided lines (A) DRO1 QTL on carrier chromosome 9 (B) DRO3 QTL on carrier chromosome 7 (C) Pup1 QTL on carrier chromosome 12 present in BC₂F₂ progenies of Maudamani/ CR3996-19-9-45-1 1 (Legend A: CR3996-19-9-45-1; Legend B: Maudamani).

Fig. 4

Ratio of deeper rooting (%) in parental lines Maudamani and CR3996-19-9-45-1 along with five pyramided lines under moisture deficient soil conditions.

Fig. 5

Phosphorus concentration (%) of leaf in parental lines Maudamani and CR3996-19-9-45-1 along with five pyramided lines under P-deficient soil conditions.

Fig. 6

Panicle photographs of parents (CR3996-19-9-45-1 and Maudamani) and their pyramided lines evaluated in BC₂F₄ generation during wet season, 2024. Numbers in the figure indicate the pyramided lines, 1: CR6508-111-101-129, 2: CR6508-111-101-267, 3: CR6508-111-101-413, 4: CR6508-111-101-537, 5: CR6508-111-101-713.

Fig. 7

Genotype-trait biplot diagram of five pyramided lines carrying DRO1, DRO3 and Pup1 QTL along with the parents for the first two principal components. DFF: Days to 50% flowering (Days); PH: Plant height (cm); TN: Tiller Number; PL: Panicle length (cm), PW: Panicle weight (g); GN: Grain Number/Panicle; CN: Chaff Number/Panicle; TGW: 1000 Grain Weight (g); L/B: L/B Ratio; M: Milling (%); HRR: Head Rice Recovery (%); AC: Amylose Content (%); GC: Gel Consistency (mm) and PY: Plot Yield (t/ha).

Fig. 8

Breeding scheme used for transfer of QTL for deeper rooting and phosphorus uptake into popular variety, ‘Maudamani’ through marker-assisted backcross breeding approach.

Fig. 9

Phenotyping for deeper rooting under moisture-deficit stress. (A) Direct sowing through open mesh wire basket in controlled tank; (B) Plants grown at seedling stage; (C) Plant response in moisture-deficit condition; (D) Dismantling of the tank and use of high-pressure water spray to remove the soil; (E) Root distribution in soil; (F) Extraction of roots along with basket; (G) Observation of root length and root angle distribution affected by the stress.

Fig. 10

Phenotyping for P-uptake in P-deficient soil. (A) Direct sowing of seeds in P-deficient soil in controlled tank; (B) Plants grown at seedling stage in P-deficient soil; (C) Plant growth at 42 DAS in P-deficient soil; (D) Plant growth at maturity stage in P-deficient condition.