Low cost high throughput image based root phenotyping pipeline for evaluation of sugarcane root system architecture under drought stress

Root System Architecture (RSA) plays an important role in the agronomic performance of a crop. Incorporation of these root traits in breeding program is hampered by the complexity in accessing the roots and its phenotyping. Lack of high throughput root phenotyping platforms for sugarcane is one of the major constraints in sugarcane root studies. In the present study an attempt was made to develop high throughput sugarcane root phenotyping pipeline comprising of a low cost plant cultivation platform and customized root image acquisition platform and image analyses using already available automated software. PVC tube system of specified dimension were used for plant growth and customized optical correction tank were used for imaging RSA. The acquired root images were fed into automated software GIAroots and about twenty quantitative root phenotype data were extracted and analysed. The working of the whole pipeline from plant growth to image analyses is demonstrated through comparative root phenotyping under drought using five genotypes of sugarcane wild relative Erianthus arundinaceus and three commercial sugarcane varieties.The relationships between the different root variables and genotypes in PCA biplots indicated high correlation among the different root traits. The study shows the low cost high throughput image based root phenotyping pipeline can be used to extract quantifiable root traits and analysed within a short span of time

Studies on association of coefficient of coancestry with progeny performance in sugarcane

The utilization of superior parental lines and identification of superior families enhance the genetic gain in sugarcane. To identify the superior parental lines and superior progenies, 1889 progenies derived from twenty crosses involving genetically diverse historical parents were evaluated for juice quality and yield attributing traits.The historical parental lines were selected based on coefficient of coancestry from the tropical and subtropical parents maintained at National Hybridization Garden. Based on progeny performance, families of Co 99006 × CoSe 92423 and Co 86032 × 85R186 were found superior for number of millable canes, , Co 86032 × 85R186 and Co 8371 × CoT 8201 for cane thickness and CoSe 95422 × Co 775 and Co 8371 × CoV 92102 for sucrose content. Parental lines such as Co 86002, Co 99006 and CoLk 98184, Co 775, 85R186 and BO 130 were identified for HR Brix; Co 419 and Co 89010, CoS 510, CoV 92102 and CoSe 92423 for cane thickness; and CoLk 94184, BO 91 and BO 32 for number of millable canes. The estimates of coefficient of coancestry was negatively correlated with HR Brix and cane thickness suggesting that parental cross combination with lesser value of coefficient of coancestry or inbreeding coefficient resulted in produce the heterotic progenies. This study based on the historic parental lines selected based on the coefficient of coancestry and inference limited to only to this experimental material. The evaluation of families derived from the population parental cross combination and parental lines in replication family block design permits the estimation of BLUP based breeding values and helpful in selection of superior parental lines and superior progenies

A Single-Tube, Functional Marker-Based Multiplex PCR Assay for Simultaneous Detection of Major Bacterial Blight Resistance Genes Xa21, xa13 and xa5 in Rice

AbstractIn marker-assisted breeding for bacterial blight (BB) resistance in rice, three major resistance genes, viz., Xa21, xa13 and xa5, are routinely deployed either singly or in combinations. As efficient and functional markers are yet to be developed for xa13 and xa5, we have developed simple PCR-based functional markers for both the genes. For xa13, we designed a functional PCR-based marker, xa13-prom targeting the InDel polymorphism in the promoter of candidate gene Os8N3 located on chromosome 8 of rice. With respect to xa5, a multiplex-PCR based functional marker system, named xa5FM, consisting of two sets of primer pairs targeting the 2-bp functional nucleotide polymorphism in the exon II of the gene TFIIAɤ5 (candidate for xa5), has been developed. Both xa13-prom and xa5FM can differentiate the resistant and susceptible alleles for xa13 and xa5, respectively, in a co-dominant fashion. Using these two functional markers along with the already reported functional PCR-based marker for Xa21 (pTA248), we designed a single-tube multiplex PCR based assay for simultaneous detection of all the three major resistance genes and demonstrated the utility of the multiplex marker system in a segregating population

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Not AvailableThe present investigation aimed to assess the nature and magnitude of genetic divergence available in the hybridization block of ICAR-Sugarcane Breeding Institute, Coimbatore and to select suitable diverse genotypes as parents for further utilization. Seventy one sugarcane parental genotypes comprising Coimbatore canes (Co canes), Co allied canes and exotic parents were explored for their genetic diversity. Fifteen traits viz., HR Brix (330 days), Brix %, Sucrose % days, Purity %, commercial cane sugar (CCS) %, cane length, cane diameter, single cane weight, number of millable canes (NMC), number of internodes, internode length, estimated cane yield and estimated commercial cane sugar yield at 300 days and brix and sucrose % at 240 days were recorded during two crop seasons (2015 and 2017). Data was subjected to cluster analysis using Mini tab software. Based on the cluster analysis, two major groups were identified which were classified into nine clusters. The cluster wise mean values indicated substantial variation among the clusters. Maximum mean value for NMC was in cluster V. Cluster IV was found to be the largest with 21 genotypes followed by cluster I with 14 genotypes and cluster II with 12 genotypes. Cluster VI had nine genotypes and Clusters VII and VIII had three genotypes each. Clusters V and IX were the smallest with a single genotype. Cluster V was most distinct cluster among the derived clusters and it showed maximum distance with clusters I, II, III, IV and IX. Other distinct cluster in this group is cluster IX and showed the maximum inter cluster distance with clusters VI, VII and VIII. Among the distinct clusters, the cluster III expressed superior performance for most of juice quality traits at 300 days while clusters I, II and cluster III showed their superiority for sucrose content at 240 days. Clusters III, IV and VI exhibited superiority for cane yield. The most divergent clusters observed were Clusters III and VI and III and VII. Minimum inter cluster distance was found between Clusters I and II. Genotypes with high inter- cluster distance can be exploited to produce more genetic variability and desirable recombinants for further improvement.Not Availabl